When I try to annotate a cDNA such as TP53 c.872_890del19, the left_align_gDNA is the genomic coordinate that describes the 3'-most change on the reverse strand. However, the left_align_cDNA is shifted -2 base pair on the positive strand rather than returning the 3'-most cDNA position on the reverse strand (which is the query).
When I try to annotate a cDNA such as TP53 c.872_890del19, the left_align_gDNA is the genomic coordinate that describes the 3'-most change on the reverse strand. However, the left_align_cDNA is shifted -2 base pair on the positive strand rather than returning the 3'-most cDNA position on the reverse strand (which is the query).
chr17:g.7577050_7577068del19/c.872890del19/p.K291Tfs*48 inside[cds_in_exon_8] CSQN=Frameshift left_align_gDNA=g.7577048_7577066del19 unaligned_gDNA=g.7577049_7577067del19 left_align_cDNA=c.870_888del19 unalign_cDNA=c.871_889del19 dbxref=GeneID:7157,HGNC:11998,MIM:191170 aliases=NP_000537 source=RefSeq
Why don't left align shifts increase the cDNA position when the gene is on the reverse strand? Thanks for your help.