Table 3.
Number of human and chimpanzee INDELs associated with retrotransposons
| Human gaps | Chimpanzee gaps | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Retrotransposon subclass | CIs | HDs | CIs + HDs | HIs | CDs | HIs + CDs | Total insertions (CIs + HIs) | Total deletions (CDs + HDs) | Total INDELs (CIs + HIs + CDs + HDs) |
| SINE | 2,264 | 1,230 | 3,494 | 5,787 | 1,234 | 7,021 | 8,051 | 2,464 | 10,515 |
| LINE | 1,311 | 536 | 1,847 | 1,756 | 296 | 2,052 | 3,067 | 832 | 3,899 |
| ERV | 208 | 311 | 519 | 156 | 200 | 356 | 364 | 511 | 875 |
| SVA | 98 | 16 | 114 | 680 | 1 | 681 | 778 | 17 | 795 |
| ME | 154 | 993 | 1,147 | 269 | 976 | 1,245 | 423 | 1,969 | 2,392 |
| Total | 4,035 | 3,086 | 7,121 | 8,648 | 2,707 | 11,355 | 12,683 | 5,793 | 18,476 |
CD = chimpanzee deletion; CI = chimpanzee insertion; ERV = endogenous retrovirus; HD = human deletion; HI = human insertion; INDEL = insertion and deletion; LINE = long interspersed nuclear element; ME = mosaic element; SINE = short interspersed nuclear element; SVA = biologically active composite elements consisting of fragments of SINE, VNTRs and Alu elements. Using Rhesus macaque as an out-group, we characterized INDEL variation as CDs, CIs, HDs or HIs.