TABLE 3.
Parameter estimates for the codon substitution models applied to the pol data
| Model | pa | Log Ld | Estimates of parametersb | Positively selected sitesc |
|---|---|---|---|---|
| M0 (1 ratio) | 1 | −2,137.255821 | ω̂ = 0.3918 | None |
| Branch specific (2 ratios) | 2 | −2,129.700900 | ω̂0 = 0.2495, ω̂1 = 1.6230 | NA |
| Site-specific | ||||
| M1, neutral (K = 2) | 1 | −2,118.947877 | p̂0 = 0.68985 (p̂1 = 0.31015) | Not allowed |
| M2, selection (K = 3) | 3 | −2,107.074525 | p̂0 = 0.67099, p̂1 = 0.32597 (p̂2 = 0.00304), ω̂2 = 52.92262 | RT, 215 (P > 99) |
| M3, discrete (K = 2) | 3 | −2,112.026513 | p̂0 = 0.93249, (p̂1 = 0.06751) ω0 = 0.17437, ω̂1 = 4.26134 | Pro, 12, 54, 72 (at 0.5 < P < 0.95), 37 (at P > 99) |
| RT, 41, 174, 177, 245 (at 0.5 < P < 0.95), 36, 135, 184, 210, 211, 215 (at P > 99) | ||||
| M3, discrete (K = 3) | 5 | −2,104.838467 | p̂0 = 0.89797, p̂1 = 0.09907, (p̂2 = 0.00297) | PRO, 10, 12, 16, 18, 38, 72, 82, (at 0.5 < P < 0.95), 37, 54, (at P > 95) |
| ω̂0 = 0.14630, ω̂1 = 2.75117, ω̂2 = 60.67074 | RT, 41, 174, 177, 204 (at 0.5 < P < 0.95), 210, 211, 215T*, 245, 36, 135, 184 (at P > 95) | |||
| M7, beta | 2 | −2,118.943419 | p̂ = 0.04111, q̂ = 0.11138 | Not allowed |
| M8, beta & ω | 4 | −2,112.028167 | p̂0 = 0.93293, p̂ = 21.08181, q̂ = 99.00000 (p̂1 = 0.06707), ω̂ = 4.27569 | Same as M3 (K = 2) |
| Branch site | ||||
| A | 3 | −2,113.535572 | p̂0 = 0.64620, p̂1 = 0.18545, (p̂2 + p̂3 = 0.16835) ω2 = 4.73987 | Sites for foreground: PRO, 10, 13, 33, 37, 38, 41, 48, 62, 82, 89 (at 0.5 < P < 0.95), 54 (at P > 95) |
| RT, 20, 44, 48, 67, 201, 208, 215, 219, 223 (at 0.5 < P < 0.95) | ||||
| B | 5 | −2,108.351559 | p̂0 = 0.77144, p̂1 = 0.04723 (p̂2 + p̂3 = 0.18132) | Sites for background: Pro, 12, 37 (at 0.5 < P < 0.95) RT, 36, 41, 135, 174, 177, 184, 204, 210, 211, 215, 245 at (0.5 < P < 0.95) |
| ω̂0 = 0.10933, ω̂1 = 4.34176, ω̂2 = 2.91030 | Sites for foreground: Pro, 10, 13, 33, 38, 41, 48, 54, 62, 72, 82, 89 (at 0.5 < P < 0.95) | |||
| RT, 20, 44, 48, 67, 201, 208, 219, 223 (at 0.5 < P < 0.95) |
a
p is the number of free parameters for the ω ratios.
b
Parameters indicating positive selection are presented in bold type. Those in parentheses are presented for clarity only but are not free parameters.
c
An asterisk indicates the site belonging to the class with p̂2 and ω̂2 in model M3 (K = 3). Underlined sites refer to positions associated with drug resistance. NA, not applicable.
d
Log L, log likelihood.