Table 1.

Putative functional SNPs associated with expression (cis-eQTLs with allele frequencies >5%; adjusted p < 0.05).

	Transcript differentially expressed	Annotation	SNP	Position SNP			Regulation	Strain Lineage	Allele frequency**
				Gene	Distance (bp) from start codon	Promoter (P)/TSS			Ancient	Modern
SNPs in upstream region	Rv0193c	1	G226676A	IGR	−105	—	Up	1	0.973	0
	Rv0326	—	T392261C	Rv0325	−12	—	Up	1,2	0.978	0.324
	Rv0377	6	T454295C	Rv0376c	−126	—	Up	1,2,4.1,4.3.4, 4.8,4.9	1	0.994
	gpdA1	4	T655986G	IGR	−37	P	Up	1,2	0.976	0.324
	mce2D	6	A690450C	mce2C	−51	—	Up	1,2	0.976	0.324
	Rv0669c	3	T769663G	IGR	−66	P	Down	4.3.3	0	0.050
	Rv0958	3	C1069871T	IGR	−12	P	Up	1.1.3	0.220	0
	Rv1096	3	T1224367C	IGR	−18	P	Down	1,2,4.1,4.3,4.8	1	0.976
	Rv1503c	1	A1694547C	IGR	−3	—	Up	1	0.973	0
	fadD31	4	T2177073C	IGR	−14	TSS/P	Down	1	0.973	0
	Rv2036	3	C2282058T	Rv2035	−41	—	Up	1.2.2*	0.157	0
	Rv2159c	1	A2421816G	Rv2160A	−151	—	Down	1,2	0.977	0.323
	PE_PGRS38	7	A2424864G	IGR	−18	TSS	Down	1	0.973	0
	Rv2712c	1	C3025431T	IGR	−103	P	Up	1	0.971	0
	vapB22	5	T3137237C	IGR	−13	P	Up	1	0.973	0
	yrbE4B	5	G3920109T	yrbE4A	−47	—	Up	1	0.971	0
	Rv3695	2	T4137190C	IGR	−16	—	Down	1	0.973	0

Table showing the candidate transcripts differentially expressed due to SNPs in upstream intergenic regions (IGRs) or within the upstream gene. Annotation of the transcript differentially expressed: 1 – Conserved hypotheticals, 2 – Cell wall and cell processes, 3 – Intermediary metabolism and respiration, 4 – Lipid metabolism, 5 – Virulence, detoxification, adaptation, 6 – Regulatory proteins, 7 – PE/PPE, 8 – information pathways. Distance of the SNP location from the start codon of the transcript is showed as negative when it is upstream and positive when it is located within the gene. TSS = Transcriptional Start Site. *Only one or two samples from the lineage out of the 3 analysed. **Allele frequency refers to the fraction of strains harbouring the SNP in a larger data set (n = 6,218)⁵⁰; “—“ when not available.