Relationship of the observed-to-expected numbers of mutations in positions with different numbers of indels. (A) Disease-associated mutations (red). (B) Non-synonymous SNPs (blue). (C) Synonymous SNPs (black). The indel index in the X-axis indicates the number of alignment gaps in the three nonhuman vertebrates included in the study. Specifically, the category 0 includes only the amino acid positions that have no indel in the multiple sequence alignments. Similarly 1, 2, and 3 includes the positions that have one, two, and three indels in the nonhuman vertebrate sequences with respect to the human sequence. Deviations from the random expectations are significant for DAMs at P < 0.01 (χ2 = 599, df = 3), significant for non-synonymous SNPs at P < 0.01 (χ2 = 143, df = 3), and not significant for synonymous SNPs (P > 0.05; χ2 = 3.7, df = 3).