Table 1.

Required genes for mycobacterial in vivo growth that contain non-synonymous SNPs in Pasteur 1173P2 and Danish 1331

No	H37Rv locus tag	Gene name	Product	Non-synonymous amino acid substitution	Pasteur 1173P2	Danish 1331
1	Rv0101	nrp	Peptide synthetase Nrp	L1365M	+	+
2	Rv0169	mce1A	Mce family protein Mce1A	S313A, P359S	+	+
3	Rv0170	mce1B	Mce family protein Mce1B	I179T	+	+
4	Rv0171	mce1C	Mce family protein Mce1C	E212D	+	+
5	Rv0176	-	Mce associated transmembrane protein	N285S, S291A	+	+
6	Rv0218	-	Transmembrane protein	C316R, D413N	+	+
7	Rv0490	senX3	Two component sensor histidine kinase SenX3	F109S	+	+
8	Rv0636	hadB	(3R)-hydroxyacyl-ACP dehydratase subunit HadB	T54A	+	+
9	Rv0643c	mmaA3	Methoxy mycolic acid synthase MmaA3	G98D	+	+
10	Rv1028c	kdpD	Sensor protein KdpD	N776D, P368S, G295D, P83S	+	+
11	Rv1109c	-	Hypothetical protein	A147T	+	+
12	Rv1128c	-	Hypothetical protein	E270G	+	+
13	Rv1204c	-	Hypothetical protein	L484I	+	+
14	Rv1224	tatB	Sec-independent protein translocase protein TatB	W8G	+	+
15	Rv1244	lpqZ	Lipoprotein LpqZ	Q242K	+	+
16	Rv1338	murI	Glutamate racemase	R154L	+	+
17	Rv1371	-	Membrane protein	I368V	+	+
18	Rv1460	-	Transcriptional regulator	I198F, A266V	+	+
19	Rv1640c	lysX	Bifunctional lysine-tRNA ligase/phosphatidylglycerol lysyltransferase	D944G, D769E	+	+
20	Rv2048c	pks12	Polyketide synthase	A4047S, P3095L, S2964R H2147Q, G1865S	+	+
21	Rv2072c	cobL	Precorrin-6Y C(5,15)-methyltransferase	L205P	+	+
22	Rv2275	-	Cyclo(L-tyrosyl-L-tyrosyl) synthase	E261A	+	+
23	Rv2359	zur	Zinc uptake regulation protein	H64R	+	+
24	Rv2374c	hrcA	Heat-inducible transcription repressor HrcA	R79Q	+	-
25	Rv2388c	hemN	Oxygen-independent coproporphyrinogen III oxidase	A184T	+	+
26	Rv2483c	plsC	Bifunctional L-3 phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase	C189G	+	+
27	Rv2502c	accD1	Acetyl/propionyl-CoA carboxylase subunit beta	F343L, G77S	+	+
27	Rv2692	ceoC	TRK system potassium uptake protein CeoC	I133V	+	+
29	Rv2696c	-	Hypothetical protein	D164N	+	+
30	Rv2702	ppgK	Polyphosphate glucokinase	I203T	+	+
31	Rv2813	-	Hypothetical protein	I76V	+	+
32	Rv2845c	proS	Proline–tRNA ligase	A232T, H177R	+	+
33	Rv2936	drrA	Daunorubicin ABC transporter ATP-binding protein DrrA	H309D	+	+
34	Rv2981c	ddlA	D-alanine–D-alanine ligase	T365A	+	+
35	Rv3042c	serB2	Phosphoserine phosphatase SerB	G116E, A70S	+	+
36	Rv3061c	fadE22	Acyl-CoA dehydrogenase FadE22	S497C, K488E	+	+
37	Rv3087	-	Diacylglycerol O-acyltransferase	L447V	+	+
38	Rv3114	-	Hypothetical protein	S11P	+	+
39	Rv3277	-	Transmembrane protein	S272L	+	+
40	Rv3335c	-	Integral membrane protein	A86V	+	+
41	Rv3371	-	Diacylglycerol O-acyltransferase	R339G, I368V	+	+
42	Rv3497c	mce4C	Mce family protein Mce4C	T46P	+	+
43	Rv3551	-	CoA-transferase subunit alpha	A7S	+	+
44	Rv3563	fadE32	Acyl-CoA dehydrogenase FadE32	Q105R, W275S	+	+
45	Rv3616c	espA	ESX-1 secretion-associated protein EspA	T192I, A4V	+	+
46	Rv3805c	aftB	Terminalbeta-(1- > 2)-arabinofuranosyltransferase	I327V	+	+
47	Rv3868	eccA1	ESX-1 secretion system protein EccA1	A243V	+	+
48	Rv3910	-	Peptidoglycan biosynthesis protein	V480A	+	+