Table 1.
Summary Statistics of the Total Number of Lineage-Specific Changes in Each Species
| Total Number of Derived Changes | ≥90% |
100% |
||
|---|---|---|---|---|
| Bonobos | Chimpanzees | Bonobos | Chimpanzees | |
| 1,267,164 | 618,150 | 1,193,455 | 520,330 | |
| Annotation category | Bonobos | Chimpanzees | Bonobos | Chimpanzees |
| 3′ UTR variant | 11,983 | 5,923 | 11,352 | 5,012 |
| 5′ UTR variant | 1,861 | 912 | 1,758 | 794 |
| Intergenic variant | 488,378 | 240,355 | 458,804 | 202,127 |
| Mature miRNA variant | 10 | 0 | 7 | 0 |
| Missense variant | 2,714 | 1,329 | 2,557 | 1,175 |
| Regulatory region variant | 170,851 | 82,425 | 161,009 | 69,786 |
| Start lost | 9 | 7 | 9 | 5 |
| Stop gained | 30 | 10 | 27 | 10 |
| Stop lost | 14 | 5 | 14 | 4 |
| Synonymous variant | 3,420 | 1,719 | 3,239 | 1,450 |
| TF binding site variant | 1,213 | 583 | 1,140 | 481 |
| Deleterious derived changes | Grantham | C-score | GWAVA | SIFT | PolyPhen-2 | GERP |
| Bonobos | 162 | 107,064 | 2,316 | 214 | 70 | 15,486 |
| Chimpanzees | 74 | 21,517 | 1,056 | 102 | 49 | 2,365 |
Note.—Number of alleles derived in one species that are fixed ancestral in the other species. ≥90% means higher than 90% allele frequency and 100% means fixed in the population. The first three rows summarize the total numbers of annotated derived alleles in each category in each population. The bottom three rows summarize the numbers of deleterious derived alleles annotated with each method, which are in high frequency in each population.