Table 3.
Chimpanzee | Rhesus macaque | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample | Genome | Sample | Genome | |||||||||
Hom | Het | Hemi | Hom | Het* | Hemi | Hom | Het | Hemi | Hom | Het* | Hemi | |
Deletions | ||||||||||||
Frameshift | 147 | 185 | 11 | 550 | 296 | 72 | 337 | 360 | 18 | 504 | 200 | 32 |
Amino acid loss | 191 | 210 | 12 | 183 | 74 | 10 | 643 | 295 | 35 | 697 | 290 | 37 |
Insertions | ||||||||||||
Frameshift | 104 | 163 | 11 | 242 | 260 | 29 | 190 | 321 | 15 | 281 | 300 | 17 |
Amino acid gain | 109 | 269 | 13 | 69 | 237 | 3 | 319 | 600 | 27 | 246 | 755 | 34 |
MNP | ||||||||||||
Synonymous | 289 | 125 | 10 | 78 | 13 | 4 | 1,310 | 318 | 81 | 963 | 52 | 41 |
Non-synonymous | 1,986 | 1,024 | 56 | 1,971 | 293 | 79 | 13,022 | 2,822 | 502 | 17,762 | 982 | 682 |
Stop codon gain | 7 | 27 | 1 | 20 | 16 | 4 | 36 | 106 | 1 | 55 | 28 | 0 |
Stop codon loss | 2 | 2 | 0 | 0 | 2 | 0 | 8 | 4 | 0 | 6 | 2 | 0 |
SNP | ||||||||||||
Synonymous | 76,204 | 14,506 | 2,355 | 75,930 | 826 | 1,864 | 318,662 | 23,085 | 11,117 | 346,779 | 2,688 | 11,653 |
Non-synonymous | 49,699 | 16,017 | 2,220 | 49,093 | 1,105 | 1,696 | 139,476 | 22,633 | 5,943 | 160,418 | 2,574 | 6,479 |
Stop codon gain | 204 | 379 | 19 | 228 | 17 | 15 | 400 | 732 | 20 | 445 | 26 | 21 |
Stop codon loss | 85 | 34 | 4 | 27 | 1 | 3 | 137 | 50 | 5 | 75 | 2 | 3 |
Genes | ||||||||||||
Deletion frameshift | 143 | 10 | 489 (678)a | 55 | 328 | 17 | 438 (579)a | 27 | ||||
Insertion frameshift | 101 | 10 | 230 (439)a | 28 | 180 | 14 | 266 (519)a | 16 | ||||
Either | 241 | 20 | 679 (1,016)a | 76 | 489 | 29 | 665 (1,013)a | 39 | ||||
Stop codon gain | 200 | 16 | 237 (259)a | 14 | 406 | 21 | 443 (494)a | 19 | ||||
Stop codon loss | 87 | 4 | 28 (32)a | 0 | 143 | 5 | 80 (84)a | 3 | ||||
Either | 280 | 19 | 263 (289)a | 14 | 534 | 26 | 513 (567)a | 22 | ||||
Any of above | 499 | 39 | 895 (1,316)a | 87 | 945 | 51 | 1082 (1,425)a | 56 |
Comparison of nucleotide level variation in sample reads and genomic cross-species alignments to human. aValues in parentheses are Hom + Het*. Hemi, hemizygous; Het, heterozygous; Hom, homozygous; MNP, multi-nucleotide polymorphism; SNP, single-nucleotide polymorphism.