Table 3.

A Set of Lineage-Specific Nonsynonymous SNPs in Virulence Genes Sufficient for the Resolution of the 18 Studied Mycobacterium tuberculosis Groups

Lineage or Sublineage	Gene	Groups	SNP	P
Beijing	mazF8	TA systems	G122T G-V	1
Beijing-modern	vapC37	TA systems	A46G T-A	1
Beijing-B0/W-148	mce3B	Cell wall proteins	T145G S-A	1
Cameroon	pcaA	Mycolic acid synthesis	C691T H-Y	1
Delhi/CAS	irtA	Metal transporter proteins	C143T A-V	0.99
EAI	irtA	Metal transporter proteins	G964T V-F	0.99
EAI-Manila	mbtB	Metal transporter proteins	G2137A D-N	1
X	pks5	Lipid and fatty acid metabolism	A3688G T-A	0.9
Ghana	yrbE3A	Cell wall proteins	G338C G-A	1
Haarlem	mgtC	Metal transporter proteins	G545A R-H	1
LAM	mce3F	Cell wall proteins	C992G P-R	1
LAM1	eccD1	Type VII secretion system	C32T T-I	1
LAM2	mmaA4	Mycolic acid synthesis	G166A E-K	1
F15/LAM4/KZN	mce3B	Cell wall proteins	T44C F-S	1
S	mazF6	TA systems	G175A G-S	1
SMI-049	pstS-1	Lipoproteins	C877G P-A	1
T-H37Rv-like	mce1F	Cell wall proteins	T1109T	1
Ural	mce3B	Cell wall proteins	C1000G Q-E	1

Note.—For every SNP, its position, nucleotide and acid change are given. Lineage T-H37Rv-like is defined by the absence of mutation in 1,109 nucleotide in mce1F. P, Pearson correlation coefficient.