FastaSeqFetcher - investigate differences between refseq and fasta exon generated transcript

[davmlaw]

NM_000399.3 - both 37/38 have last exon with CIGAR M2190 D1 M282

They have the same length but are different in the middle - RefSeq has "T" inserted at 790, CDot has an "A" inserted at 2697

The RefSeq sequence (w/poly A tail) is:

AACTGAGCGAGGAGCAATTGATTAATAGCTCGGCGAGGGGACTCACTGACTGTTATAATAACACTACACCAGCAACTCCTGGCTTCCCAGCAGCCGGAACACAGACAGGAGAGAGTCAGTGGCAAATAGACATTTTTCTTATTTCTTAAAAAACAGCAACTTGTTTGCTACTTTTATTTCTGTTGATTTTTTTTTCTTGGTGTGTGTGGTGGTTGTTTTTAAGTGTGGAGGGCAAAAGGAGATACCATCCCAGGCTCAGTCCAACCCCTCTCCAAAACGGCTTTTCTGACACTCCAGGTAGCGAGGGAGTTGGGTCTCCAGGTTGTGCGAGGAGCAAATGATGACCGCCAAGGCCGTAGACAAAATCCCAGTAACTCTCAGTGGTTTTGTGCACCAGCTGTCTGACAACATCTACCCGGTGGAGGACCTCGCCGCCACGTCGGTGACCATCTTTCCCAATGCCGAACTGGGAGGCCCCTTTGACCAGATGAACGGAGTGGCCGGAGATGGCATGATCAACATTGACATGACTGGAGAGAAGAGGTCGTTGGATCTCCCATATCCCAGCAGCTTTGCTCCCGTCTCTGCACCTAGAAACCAGACCTTCACTTACATGGGCAAGTTCTCCATTGACCCTCAGTACCCTGGTGCCAGCTGCTACCCAGAAGGCATAATCAATATTGTGAGTGCAGGCATCTTGCAAGGGGTCACTTCCCCAGCTTCAACCACAGCCTCATCCAGCGTCACCTCTGCCTCCCCCAACCCACTGGCCACAGGACCCCTGGGTGTGTGCACCATGTCCCAGACCCAGCCTGACCTGGACCACCTGTACTCTCCGCCACCGCCTCCTCCTCCTTATTCTGGCTGTGCAGGAGACCTCTACCAGGACCCTTCTGCGTTCCTGTCAGCAGCCACCACCTCCACCTCTTCCTCTCTGGCCTACCCACCACCTCCTTCCTATCCATCCCCCAAGCCAGCCACGGACCCAGGTCTCTTCCCAATGATCCCAGACTATCCTGGATTCTTTCCATCTCAGTGCCAGAGAGACCTACATGGTACAGCTGGCCCAGACCGTAAGCCCTTTCCCTGCCCACTGGACACCCTGCGGGTGCCCCCTCCACTCACTCCACTCTCTACAATCCGTAACTTTACCCTGGGGGGCCCCAGTGCTGGGGTGACCGGACCAGGGGCCAGTGGAGGCAGCGAGGGACCCCGGCTGCCTGGTAGCAGCTCAGCAGCAGCAGCAGCCGCCGCCGCCGCCGCCTATAACCCACACCACCTGCCACTGCGGCCCATTCTGAGGCCTCGCAAGTACCCCAACAGACCCAGCAAGACGCCGGTGCACGAGAGGCCCTACCCGTGCCCAGCAGAAGGCTGCGACCGGCGGTTCTCCCGCTCTGACGAGCTGACACGGCACATCCGAATCCACACTGGGCATAAGCCCTTCCAGTGTCGGATCTGCATGCGCAACTTCAGCCGCAGTGACCACCTCACCACCCATATCCGCACCCACACCGGTGAGAAGCCCTTCGCCTGTGACTACTGTGGCCGAAAGTTTGCCCGGAGTGATGAGAGGAAGCGCCACACCAAGATCCACCTGAGACAGAAAGAGCGGAAAAGCAGTGCCCCCTCTGCATCGGTGCCAGCCCCCTCTACAGCCTCCTGCTCTGGGGGCGTGCAGCCTGGGGGTACCCTGTGCAGCAGTAACAGCAGCAGTCTTGGCGGAGGGCCGCTCGCCCCTTGCTCCTCTCGGACCCGGACACCTTGAGATGAGACTCAGGCTGATACACCAGCTCCCAAAGGTCCCGGAGGCCCTTTGTCCACTGGAGCTGCACAACAAACACTACCACCCTTTCCTGTCCCTCTCTCCCTTTGTTGGGCAAAGGGCTTTGGTGGAGCTAGCACTGCCCCCTTTCCACCTAGAAGCAGGTTCTTCCTAAAACTTAGCCCATTCTAGTCTCTCTTAGGTGAGTTGACTATCAACCCAAGGCAAAGGGGAGGCTCAGAAGGAGGTGGTGTGGGGACCCCTGGCCAAGAGGGCTGAGGTCTGACCCTGCTTTAAAGGGTTGTTTGACTAGGTTTTGCTACCCCACTTCCCCTTATTTTGACCCATCACAGGTTTTTGACCCTGGATGTCAGAGTTGATCTAAGACGTTTTCTACAATAGGTTGGGAGATGCTGATCCCTTCAAGTGGGGACAGCAAAAAGACAAGCAAAACTGATGTGCACTTTATGGCTTGGGACTGATTTGGGGGACATTGTACAGTGAGTGAAGTATAGCCTTTATGCCACACTCTGTGGCCCTAAAATGGTGAATCAGAGCATATCTAGTTGTCTCAACCCTTGAAGCAATATGTATTATAAACTCAGAGAACAGAAGTGCAATGTGATGGGAGGAACATAGCAATATCTGCTCCTTTTCGAGTTGTTTGAGAAATGTAGGCTATTTTTTCAGTGTATATCCACTCAGATTTTGTGTATTTTTGATGTACACTGTTCTCTAAATTCTGAATCTTTGGGAAAAAATGTAAAGCATTTATGATCTCAGAGGTTAACTTATTTAAGGGGGATGTACATATATTCTCTGAAACTAGGATGCATGCAATTGTGTTGGAAGTGTCCTTGGTGCCTTGTGTGATGTAGACAATGTTACAAGGTCTGCATGTAAATGGGTTGCCTTATTATGGAGAAAAAAATCACTCCCTGAGTTTAGTATGGCTGTATATTTCTGCCTATTAATATTTGGAATTTTTTTTAGAAAGTATATTTTTGTATGCTTTGTTTTGTGACTTAAAAGTGTTACCTTTGTAGTCAAATTTCAGATAAGAATGTACATAATGTTACCGGAGCTGATTTGTTTGGTCATTAGCTCTTAATAGTTGTGAAAAAATAAATCTATTCTAACGCAAAACCACTAACTGAAGTTCAGATAATGGATGGTTTGTGACTATAGTGTAAATAAATACTTTTCAACAATAAAAAAAAAAAAAAA

While we generate:

AACTGAGCGAGGAGCAATTGATTAATAGCTCGGCGAGGGGACTCACTGACTGTTATAATAACACTACACCAGCAACTCCTGGCTTCCCAGCAGCCGGAACACAGACAGGAGAGAGTCAGTGGCAAATAGACATTTTTCTTATTTCTTAAAAAACAGCAACTTGTTTGCTACTTTTATTTCTGTTGATTTTTTTTTCTTGGTGTGTGTGGTGGTTGTTTTTAAGTGTGGAGGGCAAAAGGAGATACCATCCCAGGCTCAGTCCAACCCCTCTCCAAAACGGCTTTTCTGACACTCCAGGTAGCGAGGGAGTTGGGTCTCCAGGTTGTGCGAGGAGCAAATGATGACCGCCAAGGCCGTAGACAAAATCCCAGTAACTCTCAGTGGTTTTGTGCACCAGCTGTCTGACAACATCTACCCGGTGGAGGACCTCGCCGCCACGTCGGTGACCATCTTTCCCAATGCCGAACTGGGAGGCCCCTTTGACCAGATGAACGGAGTGGCCGGAGATGGCATGATCAACATTGACATGACTGGAGAGAAGAGGTCGTTGGATCTCCCATATCCCAGCAGCTTTGCTCCCGTCTCTGCACCTAGAAACCAGACCTTCACTTACATGGGCAAGTTCTCCATTGACCCTCAGTACCCTGGTGCCAGCTGCTACCCAGAAGGCATAATCAATATTGTGAGTGCAGGCATCTTGCAAGGGGTCACTTCCCCAGCTTCAACCACAGCCTCATCCAGCGTCACCTCTGCCTCCCCCAACCCACTGGCCACAGGACCCCTGGGTGGTGCACCATGTCCCAGACCCAGCCTGACCTGGACCACCTGTACTCTCCGCCACCGCCTCCTCCTCCTTATTCTGGCTGTGCAGGAGACCTCTACCAGGACCCTTCTGCGTTCCTGTCAGCAGCCACCACCTCCACCTCTTCCTCTCTGGCCTACCCACCACCTCCTTCCTATCCATCCCCCAAGCCAGCCACGGACCCAGGTCTCTTCCCAATGATCCCAGACTATCCTGGATTCTTTCCATCTCAGTGCCAGAGAGACCTACATGGTACAGCTGGCCCAGACCGTAAGCCCTTTCCCTGCCCACTGGACACCCTGCGGGTGCCCCCTCCACTCACTCCACTCTCTACAATCCGTAACTTTACCCTGGGGGGCCCCAGTGCTGGGGTGACCGGACCAGGGGCCAGTGGAGGCAGCGAGGGACCCCGGCTGCCTGGTAGCAGCTCAGCAGCAGCAGCAGCCGCCGCCGCCGCCGCCTATAACCCACACCACCTGCCACTGCGGCCCATTCTGAGGCCTCGCAAGTACCCCAACAGACCCAGCAAGACGCCGGTGCACGAGAGGCCCTACCCGTGCCCAGCAGAAGGCTGCGACCGGCGGTTCTCCCGCTCTGACGAGCTGACACGGCACATCCGAATCCACACTGGGCATAAGCCCTTCCAGTGTCGGATCTGCATGCGCAACTTCAGCCGCAGTGACCACCTCACCACCCATATCCGCACCCACACCGGTGAGAAGCCCTTCGCCTGTGACTACTGTGGCCGAAAGTTTGCCCGGAGTGATGAGAGGAAGCGCCACACCAAGATCCACCTGAGACAGAAAGAGCGGAAAAGCAGTGCCCCCTCTGCATCGGTGCCAGCCCCCTCTACAGCCTCCTGCTCTGGGGGCGTGCAGCCTGGGGGTACCCTGTGCAGCAGTAACAGCAGCAGTCTTGGCGGAGGGCCGCTCGCCCCTTGCTCCTCTCGGACCCGGACACCTTGAGATGAGACTCAGGCTGATACACCAGCTCCCAAAGGTCCCGGAGGCCCTTTGTCCACTGGAGCTGCACAACAAACACTACCACCCTTTCCTGTCCCTCTCTCCCTTTGTTGGGCAAAGGGCTTTGGTGGAGCTAGCACTGCCCCCTTTCCACCTAGAAGCAGGTTCTTCCTAAAACTTAGCCCATTCTAGTCTCTCTTAGGTGAGTTGACTATCAACCCAAGGCAAAGGGGAGGCTCAGAAGGAGGTGGTGTGGGGACCCCTGGCCAAGAGGGCTGAGGTCTGACCCTGCTTTAAAGGGTTGTTTGACTAGGTTTTGCTACCCCACTTCCCCTTATTTTGACCCATCACAGGTTTTTGACCCTGGATGTCAGAGTTGATCTAAGACGTTTTCTACAATAGGTTGGGAGATGCTGATCCCTTCAAGTGGGGACAGCAAAAAGACAAGCAAAACTGATGTGCACTTTATGGCTTGGGACTGATTTGGGGGACATTGTACAGTGAGTGAAGTATAGCCTTTATGCCACACTCTGTGGCCCTAAAATGGTGAATCAGAGCATATCTAGTTGTCTCAACCCTTGAAGCAATATGTATTATAAACTCAGAGAACAGAAGTGCAATGTGATGGGAGGAACATAGCAATATCTGCTCCTTTTCGAGTTGTTTGAGAAATGTAGGCTATTTTTTCAGTGTATATCCACTCAGATTTTGTGTATTTTTGATGTACACTGTTCTCTAAATTCTGAATCTTTGGGAAAAAATGTAAAGCATTTATGATCTCAGAGGTTAACTTATTTAAGGGGGATGTACATATATTCTCTGAAACTAGGATGCATGCAATTGTGTTGGAAGTGTCCTTGGTGCCTTGTGTGATGTAGACAATGTTACAAGGTCTGCATGTAAATGGGTTGCCTTATTATGGAGAAAAAAAATCACTCCCTGAGTTTAGTATGGCTGTATATTTCTGCCTATTAATATTTGGAATTTTTTTTAGAAAGTATATTTTTGTATGCTTTGTTTTGTGACTTAAAAGTGTTACCTTTGTAGTCAAATTTCAGATAAGAATGTACATAATGTTACCGGAGCTGATTTGTTTGGTCATTAGCTCTTAATAGTTGTGAAAAAATAAATCTATTCTAACGCAAAACCACTAACTGAAGTTCAGATAATGGATGGTTTGTGACTATAGTGTAAATAAATACTTTTCAACAATA

[davmlaw]

This has tags: gap_count=1

$ zgrep NM_000399.3 /data/annotation/cdot/refseq/GRCh38/ref_GRCh38.p2_top_level.gff3.gz 
NC_000010.11	BestRefSeq	mRNA	62811996	62816366	.	-	.	ID=rna70625;Parent=gene26267;Dbxref=GeneID:1959,Genbank:NM_000399.3,HGNC:HGNC:3239,HPRD:00551,MIM:129010;Name=NM_000399.3;Note=The RefSeq transcript has 1 non-frameshifting indel compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=EGR2;product=early growth response 2%2C transcript variant 1;transcript_id=NM_000399.3
NC_000010.11	BestRefSeq	exon	62815861	62816366	.	-	.	ID=id790321;Parent=rna70625;Dbxref=GeneID:1959,Genbank:NM_000399.3,HGNC:HGNC:3239,HPRD:00551,MIM:129010;Note=The RefSeq transcript has 1 non-frameshifting indel compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=EGR2;product=early growth response 2%2C transcript variant 1;transcript_id=NM_000399.3
NC_000010.11	BestRefSeq	exon	62811996	62814468	.	-	.	ID=id790322;Parent=rna70625;Dbxref=GeneID:1959,Genbank:NM_000399.3,HGNC:HGNC:3239,HPRD:00551,MIM:129010;Note=The RefSeq transcript has 1 non-frameshifting indel compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=EGR2;product=early growth response 2%2C transcript variant 1;transcript_id=NM_000399.3
NC_000010.11	RefSeq	cDNA_match	62815861	62816366	506	-	.	ID=aln8254;Target=NM_000399.3 1 506 +;consensus_splices=2;exon_identity=0.999664;for_remapping=1;gap_count=1;identity=0.999664;idty=1;matches=2978;num_ident=2978;num_mismatch=0;pct_coverage=100;pct_coverage_hiqual=100;pct_identity_gap=99.9664;pct_identity_ungap=100;product_coverage=1;rank=1;score=506;splices=2;weighted_identity=0.999334
NC_000010.11	RefSeq	cDNA_match	62811996	62814468	2468.76	-	.	ID=aln8254;Target=NM_000399.3 507 2978 +;consensus_splices=2;exon_identity=0.999664;for_remapping=1;gap_count=1;identity=0.999664;idty=0.999596;matches=2978;num_ident=2978;num_mismatch=0;pct_coverage=100;pct_coverage_hiqual=100;pct_identity_gap=99.9664;pct_identity_ungap=100;product_coverage=1;rank=1;score=2468.76;splices=2;weighted_identity=0.999334;Gap=M2190 D1 M282

Same issue with NM_000314.4 - seq[705] has transcript = C, genome = G -

affected cdna_match has tag: num_mismatch=1

$ zgrep NM_000314.4 ref_GRCh37.p13_top_level.gff3.gz 
NC_000010.10	BestRefSeq	mRNA	89623195	89728532	.	+	.	ID=rna41299;Name=NM_000314.4;Parent=gene20484;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89623195	89624305	.	+	.	ID=id458950;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89653782	89653866	.	+	.	ID=id458951;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89685270	89685314	.	+	.	ID=id458952;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89690803	89690846	.	+	.	ID=id458953;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89692770	89693008	.	+	.	ID=id458954;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89711875	89712016	.	+	.	ID=id458955;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89717610	89717776	.	+	.	ID=id458956;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89720651	89720875	.	+	.	ID=id458957;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	BestRefSeq	exon	89725044	89728532	.	+	.	ID=id458958;Parent=rna41299;Note=The RefSeq transcript has 1 substitution and 1 indel compared to this genomic sequence;Dbxref=GeneID:5728,Genbank:NM_000314.4,HGNC:9588,MIM:601728;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=PTEN;product=phosphatase and tensin homolog;transcript_id=NM_000314.4
NC_000010.10	RefSeq	cDNA_match	89623195	89624305	1104.71	+	.	ID=8621;Target=NM_000314.4 1 1110 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=0.9982;Gap=M666 D1 M444
NC_000010.10	RefSeq	cDNA_match	89653782	89653866	85	+	.	ID=8621;Target=NM_000314.4 1111 1195 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89685270	89685314	45	+	.	ID=8621;Target=NM_000314.4 1196 1240 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89690803	89690846	44	+	.	ID=8621;Target=NM_000314.4 1241 1284 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89692770	89693008	239	+	.	ID=8621;Target=NM_000314.4 1285 1523 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89711875	89712016	142	+	.	ID=8621;Target=NM_000314.4 1524 1665 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89717610	89717776	167	+	.	ID=8621;Target=NM_000314.4 1666 1832 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89720651	89720875	225	+	.	ID=8621;Target=NM_000314.4 1833 2057 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1
NC_000010.10	RefSeq	cDNA_match	89725044	89728532	3489	+	.	ID=8621;Target=NM_000314.4 2058 5546 +;matches=5545;identity=0.999639;splices=16;consensus_splices=16;product_coverage=1;exon_identity=0.999639;pct_identity_gap=99.9639;num_ident=5545;num_mismatch=1;pct_identity_ungap=99.982;gap_count=1;pct_coverage=100;pct_coverage_hiqual=100;weighted_identity=0.999468;rank=1;assembly_bases_seq=2050;assembly_bases_aln=2050;for_remapping=1;idty=1