TABLE 2.
Peaks of nonsynonymous nucleotide diversity for all open reading frames of SPgVver, SIVver, and DMVV-1 in South African vervet monkeysa
| Virus | ORF | Start position | Stop position | Length (no. of codons) | % of variants with nonsynonymous polymorphism |
|---|---|---|---|---|---|
| SIVver (n = 13) | gag | — | — | — | — |
| pol | — | — | — | — | |
| vif | — | — | — | — | |
| vpx | — | — | — | — | |
| tat | 5685 | 5735 | 17 | 31 | |
| 7980 | 8120 | 47 | 85 | ||
| rev | — | — | — | — | |
| env | 6107 | 6226 | 40 | 92 | |
| 6335 | 6376 | 14 | 85 | ||
| 7013 | 7078 | 22 | 62 | ||
| nef | — | — | — | — | |
| SPgVver (n = 17) | 1053 | 1082 | 10 | 24 | |
| 1326 | 1376 | 17 | 29 | ||
| 2244 | 2282 | 13 | 24 | ||
| 2403 | 2438 | 12 | 12 | ||
| 2604 | 2630 | 9 | 29 | ||
| 6696 | 6746 | 17 | 12 | ||
| 8922 | 8966 | 15 | 47 | ||
| DMVV-1 (n = 14) | 1a | 733 | 768 | 12 | 21 |
| TF | 2924 | 3064 | 47 | 71 | |
| 3152 | 3232 | 27 | 50 | ||
| 3512 | 3541 | 10 | 21 | ||
| 1b | — | — | — | — | |
| 2a′ | — | — | — | — | |
| 3′ | 11389 | 11442 | 18 | 64 | |
| 11527 | 11565 | 13 | 57 | ||
| 4′ | — | — | — | — | |
| 2a | — | — | — | — | |
| 2b | 12470 | 12526 | 19 | 79 | |
| 3 | 13201 | 13230 | 10 | 64 | |
| 4 | 13227 | 13307 | 27 | 86 | |
| 13512 | 13571 | 20 | 71 | ||
| 5a | — | — | — | — | |
| 5 | 13748 | 13849 | 34 | 79 | |
| 13922 | 13987 | 22 | 100 | ||
| 6 | — | — | — | — | |
| 7 | — | — | — | — |
a
Peaks were identified conservatively as 9-codon sliding windows in which πN exceeded both the respective window's πS and the mean value of πS for the ORF. Start and stop sites refer to approximate nucleotide coordinates in the genome sequence. Dashes indicate the absence of a nonsynonymous peak in that ORF.