Table 3 Site patterns observed across CpG censored alignments. Patterns were observed at sites classified as one of: ERV (PV); selfish DNA (RM+); or non-repetitive or repetitive but non-selfish (RM-)
From: Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split
Chimp:human | Autosomal | X-linked | ||||
|---|---|---|---|---|---|---|
| Â | PV | RM+ | RM- | PV | RM+ | RM- |
A:A | 591392 | 1603551 | 1145366 | 26509 | 83350 | 43123 |
A:T | 888 | 2496 | 1390 | 38 | 105 | 45 |
A:G | 3650 | 8749 | 5067 | 112 | 335 | 155 |
A:C | 1104 | 2678 | 1593 | 41 | 111 | 46 |
A:? | 0 | 0 | 0 | 0 | 0 | 0 |
T:A | 984 | 2572 | 1456 | 28 | 90 | 41 |
T:T | 597941 | 1609580 | 1151417 | 26035 | 87639 | 43695 |
T:G | 1197 | 2816 | 1527 | 57 | 109 | 62 |
T:C | 3636 | 8534 | 4949 | 127 | 338 | 172 |
T:? | 0 | 0 | 0 | 0 | 0 | 0 |
G:A | 3294 | 8415 | 4950 | 131 | 389 | 144 |
G:T | 1143 | 3034 | 1688 | 35 | 108 | 51 |
G:G | 450769 | 1135140 | 703983 | 22571 | 56854 | 24790 |
G:C | 974 | 2586 | 1439 | 29 | 105 | 51 |
G:? | 0 | 0 | 0 | 0 | 0 | 0 |
C:A | 1206 | 2935 | 1652 | 26 | 102 | 46 |
C:T | 3394 | 8432 | 4957 | 120 | 328 | 183 |
C:G | 986 | 2623 | 1400 | 31 | 91 | 55 |
C:C | 460550 | 1128491 | 698783 | 18236 | 56537 | 25202 |
C:? | 0 | 0 | 0 | 0 | 0 | 0 |
?:A | 5 | 0 | 2 | 0 | 0 | 0 |
?:T | 0 | 1 | 2 | 0 | 1 | 0 |
?:G | 1 | 0 | 1 | 0 | 1 | 0 |
?:C | 1 | 4 | 0 | 0 | 0 | 0 |
?:? | 0 | 0 | 0 | 0 | 0 | 0 |
total | 2123115 | 5532637 | 3731622 | 94126 | 286593 | 137861 |