. 2018 Jan 30;3(1):e00108-17. doi: 10.1128/mSystems.00108-17

TABLE 3 .

Homoplastic F_ST outliers

Location	Gene^a	Type	wcF_ST^b value for the following drug:												Known^c	Lineage
Location	Gene^a	Type	AMI	CAP	EMB	ETO	INH	KAN	MOX	OFL	PRO	PZA	RIF	STR	Known^c	Lineage
1821	dnaN	Intergenic				0.43		0.57		0.10					N	All
7570	gyrA	Missense		0.33	0.11	0.46		0.66		0.29		0.18			Y	All
7572	gyrA	Missense							0.06						Y	All
7581	gyrA	Missense							0.07						Y	All
7582	gyrA	Missense							0.35	0.22					Y	All
75233	icd2	Intergenic							0.05						N	All
94388	hycQ	Synonymous			0.07		0.12						0.12	0.13	N	All
230170	Rv0194	Missense					0.12		0.05				0.12	0.13	N	All
332916	vapC25	Missense			0.10					0.09		0.20			N	All
761155	rpoB	Missense			0.31		0.58					0.10	0.72	0.41	Y	All
761161	rpoB	Missense		0.33	0.09	0.51		0.71		0.13		0.16			Y	All
764817	rpoC	Missense	0.19												N	All
781687	rpsL	Missense			0.10		0.32					0.15		0.37	Y	All
922004	Rv0830	Missense		0.30	0.12	0.43				0.10		0.21			N	All
1076880	Rv0965c	Synonymous					0.12						0.12	0.13	N	All
1673425	fabG1	Intergenic									0.11				Y	All
1673432	fabG1	Intergenic				0.52		0.65							Y	All
1722228	pks5	Missense			0.08		0.28			0.07		0.17		0.26	N	All
2122395	lldD2	Synonymous							0.06						N	All
2155168	katG	Missense			0.36		0.89			0.13		0.32	0.60	0.66	Y	All
2174216	Rv1922	Synonymous										0.08			N	All
2207525	Rv1958c	Intergenic										0.09			N	All
2422824	Rv2161c	Missense		0.30		0.43		0.57		0.10					N	All
2660319	mbtF	Missense			0.06										N	All
2715369	Rv3413c	Intergenic	0.17		0.09		0.28						0.30	0.13	N	All
2866647	lppA	Synonymous					0.12		0.07						N	All
2867298	lppB	Synonymous					0.13								N	All
2867347	lppB	Synonymous					0.13		0.06				0.12	0.14	N	All
2867756	lppB	Synonymous					0.14								N	All
3500149	Rv3134c	Synonymous											0.11		N	All
3550789	Rv3183	Synonymous											0.12	0.13	N	All
3680932	lhr	Synonymous					0.12						0.12	0.13	N	All
4001622	fadA6	Intergenic											0.11		N	All
4247429	embB	Missense			0.25	0.45	0.23		0.05	0.11		0.31	0.21	0.20	Y	All
4247574	embB	Synonymous	0.19		0.07		0.27						0.30		Y	All
4327480	ethA	Intergenic	0.20		0.07		0.27						0.30		Y	All
764948	rpoC	Missense									0.06				Y	L2
4248003	embB	Missense		0.16											Y	L2
698	dnaA	Missense												0.10	N	L4
60185	Rv0057	Missense												0.06	N	L4
761110	rpoB	Missense	0.66												Y	L4
764822	rpoC	Missense												0.06	Y	L4
781822	rpsL	Missense					0.12						0.13	0.14	Y	L4
2123145	lldD2	Missense												0.06	N	L4
2372550	dop	Missense	0.64												N	L4
2715344	Rv2413c	Intergenic												0.06	N	L4
2986827	Rv2670c	Missense					0.16						0.17	0.15	N	L4
4247431	embB	Missense					0.11						0.11	0.07	Y	L4
4248003	embB	Missense												0.06	Y	L4

For intergenic SNPs, the closest gene is listed.

Weir and Cockerham’s F_ST (wcF_ST) values in the top 1% of values genome-wide are reported for each drug.

We identified mutations in genes previously associated with drug resistance (Y for Yes in the Known column) and novel putative resistance or compensatory mutations (N for Novel in the Known column).