Data processing flow and results of each step (i.e., numbers of SNP-transcript pairs with number of SNPs included). Numbers without brackets are numbers of SNP-transcript pairs that count the number of transcripts including an exon flanking a sdSNP if multiple transcripts are mapped over the SNP position. Brackets indicate the number of SNPs, i.e., the numbers counted uniquely based on the genome position. Parentheses in brackets (Process 5) indicate the number of sdSNPs counted in the categories of consistent and inconsistent with the GT-AG rule. This is because both alleles of these sdSNPs were included in both categories (i.e., consistent and inconsistent with the GT-AG rule) of transcript. All data in the figure are listed in Additional file 1, Table S1.