TB-Profiler

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	0.99

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rrs	1473247	n.1402C>A	non_coding_transcript_exon_variant	0.88	kanamycin	Uncertain significance	Mutation from literature
amikacin	Uncertain significance	Mutation from literature
capreomycin	Uncertain significance	Mutation from literature
rrs	1473329	n.1484G>T	non_coding_transcript_exon_variant	0.8	capreomycin	Assoc w R
kanamycin	Assoc w R
amikacin	Assoc w R

Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence
gyrA	7362	p.Glu21Gln	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	0.95	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	0.95	moxifloxacin	Not assoc w R
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
rpoB	762899	c.3093G>C	synonymous_variant	0.46	rifampicin	Not assoc w R - Interim
rpoB	762920	c.3114C>T	synonymous_variant	0.5	rifampicin	Not assoc w R - Interim
rpoB	762929	c.3123G>C	synonymous_variant	0.58	rifampicin	Not assoc w R - Interim
rpoC	762935	c.-435C>T	upstream_gene_variant	0.69	rifampicin
rpoC	763546	c.177A>G	synonymous_variant	0.56	rifampicin	Not assoc w R - Interim
rpoC	763570	c.201G>C	synonymous_variant	0.67	rifampicin	Not assoc w R - Interim
rpoC	763573	c.204G>C	synonymous_variant	0.66	rifampicin	Not assoc w R - Interim
rpoC	763594	c.225C>T	synonymous_variant	0.65	rifampicin	Not assoc w R - Interim
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	0.88	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472160	n.315C>T	non_coding_transcript_exon_variant	0.89	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472225	n.380C>G	non_coding_transcript_exon_variant	0.82	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472240	n.395G>A	non_coding_transcript_exon_variant	0.82	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472251	n.406G>C	non_coding_transcript_exon_variant	0.84	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472279	n.434T>G	non_coding_transcript_exon_variant	0.54	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472344	n.499C>T	non_coding_transcript_exon_variant	0.68	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472368	n.523A>G	non_coding_transcript_exon_variant	0.82	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472396	n.551A>T	non_coding_transcript_exon_variant	0.74	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472400	n.555C>T	non_coding_transcript_exon_variant	0.74	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472412	n.567A>G	non_coding_transcript_exon_variant	0.74	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472507	n.662C>A	non_coding_transcript_exon_variant	0.52	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472522	n.677T>G	non_coding_transcript_exon_variant	0.68	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472557	n.712G>A	non_coding_transcript_exon_variant	0.79	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472571	n.726G>T	non_coding_transcript_exon_variant	0.75	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472623	n.778A>C	non_coding_transcript_exon_variant	0.97	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472647	n.802C>T	non_coding_transcript_exon_variant	0.8	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472692	n.847T>C	non_coding_transcript_exon_variant	0.56	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472707	n.862A>T	non_coding_transcript_exon_variant	0.71	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472767	n.922G>C	non_coding_transcript_exon_variant	0.8	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472790	n.945T>C	non_coding_transcript_exon_variant	0.86	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472812	n.967A>T	non_coding_transcript_exon_variant	0.79	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472954	n.1110delC	non_coding_transcript_exon_variant	0.74	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472958	n.1113_1114insC	non_coding_transcript_exon_variant	0.7	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472973	n.1128A>T	non_coding_transcript_exon_variant	0.67	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472996	n.1151T>C	non_coding_transcript_exon_variant	0.53	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473066	n.1221A>G	non_coding_transcript_exon_variant	0.86	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473081	n.1236C>T	non_coding_transcript_exon_variant	0.65	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473145	n.1300C>T	non_coding_transcript_exon_variant	0.68	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473164	n.1319C>T	non_coding_transcript_exon_variant	0.78	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1473166	n.1321G>A	non_coding_transcript_exon_variant	0.78	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473226	n.1381C>G	non_coding_transcript_exon_variant	0.87	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473259	n.1414C>T	non_coding_transcript_exon_variant	0.83	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473315	n.1470T>C	non_coding_transcript_exon_variant	0.58	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473316	n.1471C>T	non_coding_transcript_exon_variant	0.58	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473319	n.1474C>T	non_coding_transcript_exon_variant	0.71	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473324	n.1479G>A	non_coding_transcript_exon_variant	0.81	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin
rrl	1474197	n.540C>T	non_coding_transcript_exon_variant	0.62	capreomycin	Uncertain significance
rrl	1474197	n.540C>T	non_coding_transcript_exon_variant	0.62	linezolid
rrl	1474202	n.545T>G	non_coding_transcript_exon_variant	0.75	capreomycin
rrl	1474202	n.545T>G	non_coding_transcript_exon_variant	0.75	linezolid
rrl	1474218	n.561T>G	non_coding_transcript_exon_variant	0.79	capreomycin
rrl	1474218	n.561T>G	non_coding_transcript_exon_variant	0.79	linezolid
rrl	1474253	n.596A>T	non_coding_transcript_exon_variant	0.47	capreomycin	Uncertain significance
rrl	1474253	n.596A>T	non_coding_transcript_exon_variant	0.47	linezolid	Uncertain significance
rrl	1474454	n.797G>A	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1474454	n.797G>A	non_coding_transcript_exon_variant	0.67	linezolid	Uncertain significance
rrl	1474467	n.810A>T	non_coding_transcript_exon_variant	0.64	capreomycin
rrl	1474467	n.810A>T	non_coding_transcript_exon_variant	0.64	linezolid
rrl	1474476	n.819C>T	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1474476	n.819C>T	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1474488	n.831G>A	non_coding_transcript_exon_variant	0.75	capreomycin
rrl	1474488	n.831G>A	non_coding_transcript_exon_variant	0.75	linezolid
rrl	1474496	n.839C>T	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1474496	n.839C>T	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1474497	n.840G>C	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1474497	n.840G>C	non_coding_transcript_exon_variant	0.64	linezolid	Uncertain significance
rrl	1474506	n.849C>G	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1474506	n.849C>G	non_coding_transcript_exon_variant	0.7	linezolid	Uncertain significance
rrl	1474507	n.850G>T	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1474507	n.850G>T	non_coding_transcript_exon_variant	0.7	linezolid	Uncertain significance
rrl	1474516	n.859C>T	non_coding_transcript_exon_variant	0.57	capreomycin
rrl	1474516	n.859C>T	non_coding_transcript_exon_variant	0.57	linezolid
rrl	1474552	n.895C>T	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1474552	n.895C>T	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1474558	n.901G>A	non_coding_transcript_exon_variant	0.75	capreomycin	Uncertain significance
rrl	1474558	n.901G>A	non_coding_transcript_exon_variant	0.75	linezolid
rrl	1474582	n.925T>A	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1474582	n.925T>A	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1474749	n.1092C>T	non_coding_transcript_exon_variant	0.81	capreomycin	Uncertain significance
rrl	1474749	n.1092C>T	non_coding_transcript_exon_variant	0.81	linezolid	Uncertain significance
rrl	1474752	n.1096delA	non_coding_transcript_exon_variant	0.77	capreomycin
rrl	1474752	n.1096delA	non_coding_transcript_exon_variant	0.77	linezolid
rrl	1474760	n.1103A>G	non_coding_transcript_exon_variant	0.66	capreomycin	Uncertain significance
rrl	1474760	n.1103A>G	non_coding_transcript_exon_variant	0.66	linezolid	Uncertain significance
rrl	1474823	n.1166C>G	non_coding_transcript_exon_variant	0.86	capreomycin	Uncertain significance
rrl	1474823	n.1166C>G	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1474827	n.1170C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1474827	n.1170C>T	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1474830	n.1173A>G	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1474830	n.1173A>G	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1474831	n.1174A>T	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1474831	n.1174A>T	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1474853	n.1196A>G	non_coding_transcript_exon_variant	0.81	capreomycin
rrl	1474853	n.1196A>G	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1474864	n.1207C>T	non_coding_transcript_exon_variant	0.88	capreomycin	Not assoc w R
rrl	1474864	n.1207C>T	non_coding_transcript_exon_variant	0.88	linezolid	Uncertain significance
rrl	1474904	n.1247G>C	non_coding_transcript_exon_variant	0.78	capreomycin	Uncertain significance
rrl	1474904	n.1247G>C	non_coding_transcript_exon_variant	0.78	linezolid	Uncertain significance
rrl	1474905	n.1248T>C	non_coding_transcript_exon_variant	0.78	capreomycin	Uncertain significance
rrl	1474905	n.1248T>C	non_coding_transcript_exon_variant	0.78	linezolid	Uncertain significance
rrl	1475137	n.1480A>T	non_coding_transcript_exon_variant	0.56	capreomycin	Uncertain significance
rrl	1475137	n.1480A>T	non_coding_transcript_exon_variant	0.56	linezolid	Uncertain significance
rrl	1475673	n.2016T>C	non_coding_transcript_exon_variant	0.6	capreomycin	Uncertain significance
rrl	1475673	n.2016T>C	non_coding_transcript_exon_variant	0.6	linezolid	Uncertain significance
rrl	1475699	n.2042C>T	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1475699	n.2042C>T	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1475722	n.2065G>T	non_coding_transcript_exon_variant	0.86	capreomycin
rrl	1475722	n.2065G>T	non_coding_transcript_exon_variant	0.86	linezolid
rrl	1475869	n.2212C>A	non_coding_transcript_exon_variant	0.71	capreomycin
rrl	1475869	n.2212C>A	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1475877	n.2220C>T	non_coding_transcript_exon_variant	0.73	capreomycin	Uncertain significance
rrl	1475877	n.2220C>T	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1475881	n.2224T>C	non_coding_transcript_exon_variant	0.53	capreomycin
rrl	1475881	n.2224T>C	non_coding_transcript_exon_variant	0.53	linezolid
rrl	1475883	n.2226A>T	non_coding_transcript_exon_variant	0.53	capreomycin	Uncertain significance
rrl	1475883	n.2226A>T	non_coding_transcript_exon_variant	0.53	linezolid	Uncertain significance
rrl	1475892	n.2235A>C	non_coding_transcript_exon_variant	0.68	capreomycin
rrl	1475892	n.2235A>C	non_coding_transcript_exon_variant	0.68	linezolid
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.59	capreomycin	Uncertain significance
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.59	linezolid
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.64	linezolid
rrl	1475906	n.2249C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475906	n.2249C>T	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1475916	n.2259C>T	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1475916	n.2259C>T	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1475943	n.2286G>A	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475943	n.2286G>A	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1475952	n.2295A>G	non_coding_transcript_exon_variant	0.79	capreomycin	Uncertain significance
rrl	1475952	n.2295A>G	non_coding_transcript_exon_variant	0.79	linezolid	Uncertain significance
rrl	1476194	n.2537A>T	non_coding_transcript_exon_variant	0.87	capreomycin
rrl	1476194	n.2537A>T	non_coding_transcript_exon_variant	0.87	linezolid
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.82	capreomycin	Not assoc w R
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1476201	n.2544C>T	non_coding_transcript_exon_variant	0.81	capreomycin	Not assoc w R
rrl	1476201	n.2544C>T	non_coding_transcript_exon_variant	0.81	linezolid	Uncertain significance
rrl	1476204	n.2547C>T	non_coding_transcript_exon_variant	0.81	capreomycin
rrl	1476204	n.2547C>T	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.81	capreomycin	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.81	linezolid	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1476252	n.2595T>G	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1476252	n.2595T>G	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1476256	n.2599A>G	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1476256	n.2599A>G	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.79	capreomycin	Not assoc w R
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.79	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.57	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.57	linezolid	Uncertain significance
rrl	1476363	n.2706A>G	non_coding_transcript_exon_variant	0.57	capreomycin
rrl	1476363	n.2706A>G	non_coding_transcript_exon_variant	0.57	linezolid
rrl	1476366	n.2709A>C	non_coding_transcript_exon_variant	0.54	capreomycin
rrl	1476366	n.2709A>C	non_coding_transcript_exon_variant	0.54	linezolid
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.54	capreomycin	Uncertain significance
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.54	linezolid
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.5	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.5	linezolid	Uncertain significance
rrl	1476374	n.2717T>G	non_coding_transcript_exon_variant	0.72	capreomycin
rrl	1476374	n.2717T>G	non_coding_transcript_exon_variant	0.72	linezolid
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.93	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.93	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.86	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
fbiB	3642877	p.Lys448Arg	missense_variant	0.91	clofazimine	Uncertain significance
					pretomanid
					delamanid	Uncertain significance
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin	rrs	n.1402C>A	Uncertain significance	Mutation from literature
amikacin	rrs	n.1484G>T	Assoc w R
capreomycin	rrs	n.1402C>A	Uncertain significance	Mutation from literature
capreomycin	rrs	n.1484G>T	Assoc w R
kanamycin	rrs	n.1402C>A	Uncertain significance	Mutation from literature
kanamycin	rrs	n.1484G>T	Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

TB-Profiler result