Error, chr discrepancy in gtf info for chrY HAVANA exon 386368 386907 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 1; exon_id "ENSE00001912068.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,386368,386907,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 386368 386691 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 1; exon_id "ENSE00001912068.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,386368,386691,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361590 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 361405 361590 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 3; exon_id "ENSE00003509428.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 347590 347693 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 3; exon_id "ENSE00003509428.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 4; exon_id "ENSE00003492683.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 347234 347336 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 4; exon_id "ENSE00003492683.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346701 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 5; exon_id "ENSE00003489026.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 346701 346775 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 5; exon_id "ENSE00003489026.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346260 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 6; exon_id "ENSE00003574906.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 346174 346260 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 6; exon_id "ENSE00003574906.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 7; exon_id "ENSE00003687848.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 345516 345672 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 7; exon_id "ENSE00003687848.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341883 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 8; exon_id "ENSE00003511595.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 341883 341931 . - 2 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 8; exon_id "ENSE00003511595.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341396 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 9; exon_id "ENSE00003587700.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 341307 341396 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 9; exon_id "ENSE00003587700.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 10; exon_id "ENSE00003668507.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 340765 340940 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 10; exon_id "ENSE00003668507.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338778 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 11; exon_id "ENSE00003622978.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 338778 338896 . - 2 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 11; exon_id "ENSE00003622978.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338604 338710 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 12; exon_id "ENSE00003501875.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338604,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 338604 338710 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 12; exon_id "ENSE00003501875.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338604,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 333933 334517 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 13; exon_id "ENSE00001844596.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,333933,334517,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 334370 334517 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 13; exon_id "ENSE00001844596.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,334370,334517,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341711 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 1; exon_id "ENSE00001918099.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341711,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 2; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338778 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 3; exon_id "ENSE00003592960.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338604 338710 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 4; exon_id "ENSE00003534283.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338604,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 334235 334517 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 5; exon_id "ENSE00001489278.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,334235,334517,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347324 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 1; exon_id "ENSE00001716328.2"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347324,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346701 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 2; exon_id "ENSE00003571094.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346260 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 3; exon_id "ENSE00003477290.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 4; exon_id "ENSE00003641725.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 5; exon_id "ENSE00001915623.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 6; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338778 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 7; exon_id "ENSE00003592960.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 334239 338710 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 8; exon_id "ENSE00001815257.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,334239,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345629 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 1; exon_id "ENSE00001890387.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345629,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341883 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 2; exon_id "ENSE00003555172.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341396 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 3; exon_id "ENSE00003689816.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 4; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338613 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 5; exon_id "ENSE00001951758.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338613,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345626 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 1; exon_id "ENSE00001888244.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345626,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341883 342237 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 2; exon_id "ENSE00001815626.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,342237,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341396 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 3; exon_id "ENSE00003689816.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 4; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346514 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477636.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-207"; exon_number 1; exon_id "ENSE00001896157.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055581.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346514,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477636.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-207"; exon_number 2; exon_id "ENSE00003641725.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055581.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341911 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477636.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-207"; exon_number 3; exon_id "ENSE00001911121.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055581.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341911,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 386368 386955 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 1; exon_id "ENSE00001912680.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,386368,386955,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 362255 362332 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 2; exon_id "ENSE00001847312.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,362255,362332,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361590 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 3; exon_id "ENSE00003585491.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 4; exon_id "ENSE00003475055.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 5; exon_id "ENSE00003606316.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346701 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 6; exon_id "ENSE00003571094.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346260 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 7; exon_id "ENSE00003477290.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 344896 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 8; exon_id "ENSE00001950030.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,344896,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361516 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 1; exon_id "ENSE00001916804.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361516,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 2; exon_id "ENSE00003475055.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 3; exon_id "ENSE00003606316.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346637 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 4; exon_id "ENSE00001851476.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346637,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347838 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000475859.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-205"; exon_number 1; exon_id "ENSE00001843788.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354556.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347838,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000475859.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-205"; exon_number 2; exon_id "ENSE00003606316.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354556.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346720 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000475859.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-205"; exon_number 3; exon_id "ENSE00001849084.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354556.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346720,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 373532 374044 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 1; exon_id "ENSE00001489321.3"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,373532,374044,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 373532 373771 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 1; exon_id "ENSE00001489321.3"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,373532,373771,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361590 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 361405 361590 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347611 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 3; exon_id "ENSE00001877883.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347611,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 347611 347693 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 3; exon_id "ENSE00001877883.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347611,347693,-";
Done.
-parsing GTF file: /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:10:32 : INFO : Done.
-parsing GTF file: /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[690000] -done parsing /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
'excessive soft clipping' => 4898,
'num genes matched < 2' => 168,
'seq-similar region overlap' => 21,
'per_id < 96' => 2740,
'low complexity anchor region' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 63,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 22,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
' ** passed ** ' => 1339
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[20000] -fusion SPANNING read extraction for scaff: CCNY--AL353600.2
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[114000] -fusion SPANNING read extraction for scaff: RAP1B--SRGAP1
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[46000]
[47000]
[48000] -fusion SPANNING read extraction for scaff: VGLL4--ATG7
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 15024,
'seq similar region alignment' => 495
};
EM: Starting log likelihood: -2164.405859
EM: Round [1] log likelihood: -2163.761580
EM: Round [2] log likelihood: -2163.359857
EM: Round [3] log likelihood: -2163.041851
EM: Round [4] log likelihood: -2162.784548
EM: Round [5] log likelihood: -2162.574075
EM: Round [6] log likelihood: -2162.400463
EM: Round [7] log likelihood: -2162.256305
EM: Round [8] log likelihood: -2162.135965
EM: Round [9] log likelihood: -2162.035072
EM: Round [10] log likelihood: -2161.950185
EM: Round [11] log likelihood: -2161.878554
EM: Round [12] log likelihood: -2161.817962
EM: Round [13] log likelihood: -2161.766604
EM: Round [14] log likelihood: -2161.722999
EM: Round [15] log likelihood: -2161.685924
EM: Round [16] log likelihood: -2161.654362
EM: Round [17] log likelihood: -2161.627467
EM: Round [18] log likelihood: -2161.604529
EM: Round [19] log likelihood: -2161.584951
EM: Round [20] log likelihood: -2161.568230
EM: Round [21] log likelihood: -2161.553943
EM: Round [22] log likelihood: -2161.541729
EM: Round [23] log likelihood: -2161.531284
EM: Round [24] log likelihood: -2161.522348
EM: Round [25] log likelihood: -2161.514701
EM: Round [26] log likelihood: -2161.508156
EM: Round [27] log likelihood: -2161.502553
EM: Round [28] log likelihood: -2161.497756
EM: Round [29] log likelihood: -2161.493647
EM: Round [30] log likelihood: -2161.490128
EM: Round [31] log likelihood: -2161.487114
EM: Round [32] log likelihood: -2161.484531
EM: Round [33] log likelihood: -2161.482319
EM: Round [34] log likelihood: -2161.480424
EM: Round [35] log likelihood: -2161.478799
EM: Round [36] log likelihood: -2161.477408
EM: Round [37] log likelihood: -2161.476215
EM: Round [38] log likelihood: -2161.475193
EM: Round [39] log likelihood: -2161.474317
EM: Round [40] log likelihood: -2161.473567
EM: Round [41] log likelihood: -2161.472924
EM: Round [42] log likelihood: -2161.472372
EM: Round [43] log likelihood: -2161.471900
EM: Round [44] log likelihood: -2161.471495
EM: Round [45] log likelihood: -2161.471148
EM: Round [46] log likelihood: -2161.470850
EM: Round [47] log likelihood: -2161.470595
EM: Round [48] log likelihood: -2161.470377
EM: Round [49] log likelihood: -2161.470189
EM: Round [50] log likelihood: -2161.470029
EM: Round [51] log likelihood: -2161.469891
EM: Round [52] log likelihood: -2161.469773
EM: Round [53] log likelihood: -2161.469672
EM: Round [54] log likelihood: -2161.469586
EM: Stopping iterations at round 54 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2116.860461
EM: Round [1] log likelihood: -2116.859622
EM: Round [2] log likelihood: -2116.859619
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 294936328
Warning - not locating file: /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
ls: cannot access 'IGV_inputs': No such file or directory