. 2019 Mar 26;9:5204. doi: 10.1038/s41598-019-41692-2

Table 2.

Non-synonymous variants in transcriptional regulatory genes with eQTL associations, with potential functional impairment.

Gene	Mutation	Family	Lineage of strains carrying mutation	Allele frequency
Gene	Mutation	Family	Lineage of strains carrying mutation	Ancient	Modern
whiB5	S21G	whiB	1.2.2**	0.021	0
Rv0023	G217D		4.9**	0	0.001
Rv0042c	L186R*	MarR	4.9**	0	0
Rv0144	P36L*	tetR	4.9**	0	0
Rv0195	C41STOP	LuxR	1.2.2**	0.021	0
Rv0275c	S24L	tetR	1	0.973	0
iniR	E23K		1.2.2**	0.019	0
Rv0377	P302R*	LysR	1	0.973	0
Rv0386	L475R*	LuxR/UhpA	4.1.1.3	0	0.003
ramB	P91Q		1	0.973	0
	T118A		4.9**	0	0.001
	Q121R		1	0.973	0
Rv0576	R233H*	ArsR	1,2	0.978	0.334
Rv0691c	A140T		2	0.003	0.114
Rv0818	P227L*		4.1.1.3	0	0.003
Rv0818	E246K*		4.1.2	0	0.009
narL	G169R*		2	0.003	0.147
Rv0890c	E234G*	LuxR	2	0.003	0.111
Rv0890c	E303K*	LuxR	4.1.2	0	0.009
Rv0891c	V37G*		1,2,4.1,4.3,4.8	1	0.974
kdpE	G60S*	KDPD/KDPE	2	0.003	0.111
Rv1219c	R11T		1.2.2**	0.148	0
embR	A70S		4.1.2	0	0.009
embR	C110Y		1	0.973	0
Rv1453	D208N		1.1.3	0.230	0
	D218N		1.2.2**	0.021	0
	P405Q		1,2,4.1,4.3,4.8	1	0.974
Rv1674c	E189G*		4.3	0.014	0.281
cmr	V59A	CRP/FNR	1	0.974	0
cmr	A125S	CRP/FNR	1.1.3*	0.072	0
Rv1776c	R154S		1.2.2**	0.019	0
blaI	L57R		1	0.970	0
mce3R	D148Y*	tetR	1.1.3**	—	—
Rv2017	A262E		1,2,4.1,4.3,4.8	0.998	0.973
Rv2160A	C155R	tetR	1,2	0.977	0.323
zur	H64R*		1	0.973	0
Rv2488c	D184Y*	LuxR	1.2.2**	0.018	0
Rv2621c	A110V		2	0.003	0.148
sirR	Q131STOP		1	0.973	0
Rv3060c	G420D	GntR	4.1.2	0	0.009
virS	L316R*	AraC/XylS	1	0.973	0
Rv3167c	P17Q	tetR	1	0.973	0
Rv3249c	T154A	tetR	4.1.1.3	0.003	0.049
whiB4	S2L	whiB	1.1.3	0.223	0
Rv3736	G144R*	AraC/XylS	1	0.971	0
whiB6	G71D	whiB	1.2.2**	0.014	0

Table showing non-synonymous mutations in transcriptional regulatory genes found as potential eQTLs. *Sorting Intolerant from tolerant (SIFT) predicted scores (p value) < 0.05 and considered to have functional impact; whilst for the others the SIFT software was unable to predict functional effects of mutations; **Only one or two samples available from the lineage. Allele frequency refers to the fraction of strains harbouring the SNP in a larger data set (n = 6,218)²⁶.