Table 1.
Gene | Locus | No. SNPs | Diversity π | phi p-value | phi p-valuea | dN/dS (w) | No. sitesb | Lineage specific phi |
---|---|---|---|---|---|---|---|---|
Rv0030 | Rv0030 | 3 | 0.0033 | 1.000 | 1.000 | - | 0 | - |
Rv0095c | Rv0095c | 10 | 0.0059 | 0.005 | 0.021 | 10.13 | 3 | - |
Rv0182c | sigG | 3 | 0.0003 | 0.046 | 0.046 | - | 0 | - |
Rv0278c | pe_pgrs3 | 130 | 0.0193 | <0.001 | <0.001 | 10.5 | 49 | 1,3,4 |
Rv0279c | pe_pgrs4 | 49 | 0.0035 | 0.001 | 0.419 | 10.5 | 20 | - |
Rv0282 | eccA3 | 5 | 0.0005 | 0.007 | 0.210 | 9.697 | 6 | - |
Rv0850 | Rv0850 | 2 | 0.0031 | 1.000 | 1.000 | 9.264 | 4 | - |
Rv0978c | pe_pgrs17 | 9 | 0.0005 | 0.003 | 1.000 | 10.495 | 9 | - |
Rv1148c | Rv1148c | 18 | 0.0022 | <0.001 | 0.015 | 10.492 | 5 | 4 |
Rv1793 | esxN | 6 | 0.0023 | 0.034 | 0.159 | 9.694 | 2 | 4 |
Rv1945 | Rv1945 | 18 | 0.0010 | <0.001 | 0.026 | 10.433 | 5 | - |
Rv2048c | pks12 | 80 | 0.0008 | <0.001 | 0.012 | 10.5 | 79 | 4 |
Rv2543 | lppA | 8 | 0.0015 | 0.006 | 0.002 | 10.036 | 5 | 4 |
Rv2544 | lppB | 60 | 0.0123 | <0.001 | <0.001 | 5.336 | 33 | 1,2,4 |
Rv3425 | ppe57 | 31 | 0.0154 | 0.431 | 1.000 | 10.5 | 21 | - |
Rv3429 | ppe59 | 19 | 0.0041 | <0.001 | 0.084 | 10.419 | 29 | 4 |
Rv3466 | Rv3466 | 6 | 0.0010 | 0.004 | 0.373 | 7.757 | 3 | - |
Rv3478 | ppe60 | 105 | 0.0061 | <0.001 | 0.004 | 7.502 | 54 | 4 |
Rv3619c | esxV | 3 | 0.0022 | 0.025 | 1.000 | 10.391 | 2 | - |
π nucleotide diversity, phi recombination, NS not significant
aafter removing sites under selection
bnumber of sites under selection using the Bayes Empirical Bayes method
Bolded refers to π > 0.003 or phi p-value < 0.05