Table 5. Likelihood scores and parameter estimates for STB PE/PE_PGRS genes assuming the F3x4 model of codon frequencies.
| Modela | Log Likelihood | Parameter estimatesa | Positively selected sites (BEB)b |
| PE4 | |||
| M1a: neutral | −1975.596593 | p0 = 0.91590, p1 = 0.08410 | |
| M2a: selection | −1969.253305 | p0 = 0.99765, p1 = 0.00000, | 115 L (0.958) |
| p2 = 0.00235, ω2 = 10.68754 | |||
| M7: beta | −1975.658356 | p = 0.005, q = 0.04827 | |
| M8a: beta and ω = 1 | −1975.596586 | p0 = 0.91591, p1 = 0.08409, | Not allowed |
| p = 0.00500, q = 1.05450 | |||
| M8: beta and ω | −1969.286308 | p0 = 0.99768, p = 0.18993 | 115 L (0.962) |
| q = 2.31635, ω = 11.53154 | |||
| PE_PGRS62 | |||
| M1a: neutral | −1966.440204 | p0 = 0.50190, p1 = 0.49810 | |
| M2a: selection | −1960.179961 | p0 = 0.95359, p1 = 0.00000, | |
| p2 = 0.04641 | |||
| ω0 = 0.00000, ω1 = 1.00000, | |||
| ω2 = 28.99320 | |||
| M7: beta | −1967.313763 | p = 0.43253, q = 0.00500 | |
| M8a: beta and ω = 1 | −1966.440201 | p0 = 0.50190, p1 = 0.49810, | |
| p = 0.00500, q = 1.36371 | |||
| M8: beta and ω | −1960.179961 | p0 = 0.95359, p = 0.00500, | 106 Q (0.943) |
| q = 85.54963, ω = 28.99244 | 253 N (0.942) | ||
| 307 Q (0.944) |
a
p and q are parameters of the beta distribution. p0 = proportion of sites falling into nearly neutral site class, p 1 = proportion of sites falling into neutral site class, p 2 = proportion of sites falling into positively selected site class.
b
Sites (relative to H37Rv'corresponding gene numbering) falling into positively selected class with BEB estimates>0.90 are listed.