Table 1.

Loci that are highly diverse, with recombination, or under selective pressure

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