Difference in splice site score between two alleles. sdSNPs were categorized according to flanking exon types and SNP allele prediction. When only one allele of a sdSNP was consistent with the GT-AG rule in every transcript, the sdSNPs was defined as "constantly consistent" (blue), and those that were inconsistent with the rule in every transcript were defined as "constantly inconsistent" (pink). When both alleles of a sdSNP were predicted (i.e., one allele was predicted to be consistent with the GT-AG rule in some transcripts, but the other allele of the identical SNP was predicted to be inconsistent in the other transcript), the sdSNP was defined as "both cases" (purple). The six sdSNPs at CE dinucleotides were predicted to be "both cases," while no "both cases" was predicted for sdSNPs at AE dinucleotides (Process 5 in Figure 2). Numbers in parentheses are numbers of cases and percentages. Average differences of the score in sdSNPs at AE and CE dinucleotides are depicted right and left of the thick vertical bar, respectively.