TABLE 3.

Summary of SNPs analyzed by filtering phylogenetic alignments for similar intron/exon architecture

“Splice altering SNPs” represent SNPs that did not occur in the alignment of organisms with similar intron/exon architecture or, if they occurred, only occurred alongside other mutations within a 6-mer (possible compensatory mutations). “Neutral SNPs” were SNPs that had SNP occurrences without mutations in the surrounding hexamer. The classes of coding exons and exons derived from non-coding genes or single exon genes' exons were found to be independent by a χ² test (p < 0.05). The SNP identities for all groups are listed in supplemental Table S1.

Data set	Splice altering SNPs	Neutral SNPs
Disease associated and random synonymous SNPs	45% (29)	55% (36)
Randomly selected noncoding exonic or single exon SNPs	30% (34)	70% (80)
p < 0.05 between the two SNP datasets