The Supporting Tables contain tab-delimited files that can be copied into spreadsheets.

Table S2: 61 Single nucleotide polymorphisms and RD 131 (number 36) used in this study

Position in matrix (Figure 1)	Position in H37Rv	Reference 	Synonymous (s) nonsynonymous (ns)	Gene name	Polymorphism
1	4026899	this study	s	radA	G/A
2	725190	this study	s	recC	G/A
3	4182387	this study	s	ligC	G/C
4	4166441	this study	s	dnaZX	G/A
5	4400839	this study	s	sigM	T/C
6	15890	this study	s	pknB	G/A
7	252900	this study	s	pckA	C/T
8	2602454	this study	s	narK1	T/G
9	3147511	this study	s	infB	T/G
10	1511460	this study	s	fadE14	C/T
11	3569508	this study	s	uvrD2	G/A
12	2733931	this study	s	rbsK	A/C
13	3985254	this study	s	cyp125	G/T
14	2178823	this study	s	fadD31	C/T
15	553861	this study	s	lpd	G/A
16	2493394	this study	s	glnA2	G/A
17	1759521	this study	s	frdB	C/T
18	516203	this study	s	xthA	C/T
19	647110	this study	s	menD	G/A
20	2092763	this study	s	guaB1	G/T
21	1306514	this study	s	fadH	G/A
22	4158493	this study	s	cobQ2	C/T
23	1127493	this study	s	tatD	T/C
24	441823	this study	s	fba	C/T
25	4218941	this study	s	echA21	G/A
26	146236	this study	s	fusA2	C/G
27	2321975	this study	s	cobG	T/C
28	2235087	this study	s	ctpG	G/A
29	1477596	this study	s	ogt	C/T
30	605150	this study	s	hemB	G/A
31	2774555	this study	ns	aglA	T/C
32	3813266	[31]	s	guaA	C/T
33	1364706	[31]	s	sigE	G/A
34	2668467	[31]	s	mbtD	G/A
35	2472610	[31]	s	cobS	C/T
37	2987114	[31]	s	ribD	C/T
38	1260012	[31]	s	metE	C/A
39	2389269	[31]	s	ansP	G/A
40	151798	[31]	s	pepA	A/G
41	1152701	[31]	s	kdpA	C/T
42	1145736	[31]	s	eno	T/A
43	2291161	this study	s	lipT	C/T
44	861277	this study	s	aldA	C/T
45	3707236	this study	s	sdhB	G/T
46	4025853	this study	s	lpqE	G/T
47	3671786	this study	s	lat	G/C
48	4248115	this study	s	embB	C/T
49	4109342	this study	s	acs	G/A
50	2034070	this study	s	mycP5	A/C
51	144699	this study	s	fadD7	C/A
52	3709472	this study	s	moaX	C/G
53	3075639	this study	s	fabG	T/C
54	2916854	this study	s	gabT	C/G
55	870019	this study	s	purB	C/T
56	3433281	this study	s	pgmA	G/C
57	2505016	this study	s	cobC	C/T
58	1778323	this study	s	bioD	G/A
59	3904061	this study	s	cpsA	G/A
60	2726636	this study	s	ahpC	G/A
61	3620430	this study	s	secA1	G/C
62	1978776	this study	s	fadD1	A/G