Table 1. Characteristics of nSNP-containing genes identified in initial M. tuberculosis inoculum population.

Mutation nature	Locus tag	Protein name	Amino acid substitution	Putative function	Functional Category	Amino acid change tolerance
nSNP	Rv0282	EccA3	V482G	ESX-3 secretion system protein	Transport	Deleterious
nSNP	Rv0422c	ThiD	Q21K	Thiamine metabolism	Metabolism	Deleterious
nSNP	Rv0467	Icl1	A148G	Glyoxylate - dicarboxylate metabolism	Metabolism	Deleterious
nSNP	Rv0587	YrbE2A	V146G	ABC - phospholipid transporters	Transport	Deleterious
nSNP	Rv0969	CtpV	A490P	Cation-transporting ATPase	Transport	Deleterious
nSNP	Rv1248c	Kgd	T675P	Alternate tricarboxylic acid cycle	Metabolism	Deleterious
nSNP	Rv1307	AtpH	V241G	Oxidative phosphorylation	Metabolism	Deleterious
nSNP	Rv1384	CarB	A860G	Pyrimidine metabolism - alanine, aspartate - glutamate metabolism	Metabolism	Deleterious
nSNP	Rv1661	Pks7	R808P	Lipid biosynthesis proteins - polyketide synthase	Metabolism	Deleterious
nSNP	Rv1666c	Cyp139	V1G	Bisphenol, aminobenzoate, limonene and pinene degradation	Metabolism	Neutral
nSNP	Rv1695	PpnK	V294G	Nicotinate - nicotinamide metabolism	Metabolism	Deleterious
nSNP	Rv1956	HigA	V96G	Antitoxin	Detoxification	Neutral
nSNP	Rv2143	Hypothetical protein	H106P	Putative phosphoribosyl transferase	Metabolism	Neutral
nSNP	Rv2290	LppO	Y125S	Lipoprotein	Cell wall	Deleterious
nSNP	Rv2395	Hypothetical protein	S625P	Unknown	Transport	Deleterious
nSNP	Rv2682c	Dxs1	A424P	Thiamine metabolism - terpenoid biosynthesis	Metabolism	Neutral
nSNP	Rv2724c	FadE20	N245T	Oxidoreductases - geraniol degradation	Metabolism	Deleterious
nSNP	Rv2809	Hypothetical protein	N57T	Unknown	Unknown	Deleterious
nSNP	Rv3091	Hypothetical protein	H217P	Unknown	Unknown	Neutral
nSNP	Rv3270	CtpC	A166E	Manganese/zinc-exporting P-type ATPase	Transport	Deleterious
nSNP	Rv3313c	Add	S325G	Purine metabolism	Metabolism	Neutral
nSNP	Rv3584	LpqE	V95G	Lipoprotein	Cell wall	Deleterious
nSNP	Rv3691	Hypothetical protein	A62G	Unknown	Unknown	Neutral
nSNP	Rv2157c*	murF	L399V	Lysine biosynthesis - peptidoglycan biosynthesis - vancomycin resistance	Cell wall	Deleterious
nSNP	Rv0272c*	Hypothetical protein	H91R	Putative serine aminopeptidase	Unknown	Neutral