TB-Profiler

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.8	Euro-American (mainly T)	RD219	1.0

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rrs	1473247	n.1402C>A	non_coding_transcript_exon_variant	0.42	amikacin	Uncertain significance	Mutation from literature
capreomycin	Uncertain significance	Mutation from literature
kanamycin	Uncertain significance	Mutation from literature

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
rpoC	762899	c.-471G>T	upstream_gene_variant	0.24	rifampicin
rpoB	762920	c.3114C>T	synonymous_variant	0.29	rifampicin	Not assoc w R - Interim
rpoB	762929	c.3123G>C	synonymous_variant	0.3	rifampicin	Not assoc w R - Interim
rpoC	762959	c.-411G>T	upstream_gene_variant	0.39	rifampicin
rpoC	762971	c.-399G>C	upstream_gene_variant	0.29	rifampicin
rpoC	763528	c.159G>A	synonymous_variant	0.38	rifampicin	Not assoc w R - Interim
rpoC	763534	c.165T>C	synonymous_variant	0.43	rifampicin
rpoC	763537	c.168C>G	synonymous_variant	0.41	rifampicin
rpoC	763546	c.177A>G	synonymous_variant	0.39	rifampicin	Not assoc w R - Interim
rpoC	763570	c.201G>C	synonymous_variant	0.53	rifampicin	Not assoc w R - Interim
rpoC	763573	c.204G>C	synonymous_variant	0.5	rifampicin	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	0.92	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	0.92	clofazimine	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
fbiC	1303747	p.Thr273Ala	missense_variant	1.0	pretomanid
					delamanid	Uncertain significance
					clofazimine	Uncertain significance
rrs	1472122	n.277G>T	non_coding_transcript_exon_variant	0.44	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472123	n.278A>T	non_coding_transcript_exon_variant	0.5	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472124	n.279C>T	non_coding_transcript_exon_variant	0.44	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	0.48	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472160	n.315C>T	non_coding_transcript_exon_variant	0.61	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472225	n.380C>G	non_coding_transcript_exon_variant	0.48	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472368	n.523A>G	non_coding_transcript_exon_variant	0.33	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472507	n.662C>A	non_coding_transcript_exon_variant	0.48	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472522	n.677T>G	non_coding_transcript_exon_variant	0.5	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472557	n.712G>A	non_coding_transcript_exon_variant	0.59	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472571	n.726G>T	non_coding_transcript_exon_variant	0.52	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472581	n.736A>C	non_coding_transcript_exon_variant	0.47	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472582	n.737G>T	non_coding_transcript_exon_variant	0.48	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472584	n.739A>T	non_coding_transcript_exon_variant	0.48	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472585	n.740A>C	non_coding_transcript_exon_variant	0.5	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472623	n.778A>C	non_coding_transcript_exon_variant	0.6	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472647	n.802C>T	non_coding_transcript_exon_variant	0.66	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472673	n.828T>G	non_coding_transcript_exon_variant	0.67	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472707	n.862A>T	non_coding_transcript_exon_variant	0.77	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472767	n.922G>C	non_coding_transcript_exon_variant	0.71	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472790	n.945T>C	non_coding_transcript_exon_variant	0.56	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472812	n.967A>T	non_coding_transcript_exon_variant	0.52	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472954	n.1110delC	non_coding_transcript_exon_variant	0.68	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472958	n.1113_1114insC	non_coding_transcript_exon_variant	0.62	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472973	n.1128A>T	non_coding_transcript_exon_variant	0.79	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472986	n.1141_1142insA	non_coding_transcript_exon_variant	0.71	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472989	n.1145delA	non_coding_transcript_exon_variant	0.73	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472996	n.1151T>C	non_coding_transcript_exon_variant	0.79	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473145	n.1300C>T	non_coding_transcript_exon_variant	0.36	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473164	n.1319C>T	non_coding_transcript_exon_variant	0.44	kanamycin
					capreomycin
					streptomycin	Uncertain significance
					amikacin
rrs	1473166	n.1321G>A	non_coding_transcript_exon_variant	0.39	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473226	n.1381C>G	non_coding_transcript_exon_variant	0.54	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473276	n.1431A>G	non_coding_transcript_exon_variant	0.34	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473288	n.1443C>G	non_coding_transcript_exon_variant	0.31	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473290	n.1445C>T	non_coding_transcript_exon_variant	0.32	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1473292	n.1447G>T	non_coding_transcript_exon_variant	0.33	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473294	n.1449A>G	non_coding_transcript_exon_variant	0.36	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473301	n.1456T>C	non_coding_transcript_exon_variant	0.38	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1474558	n.901G>A	non_coding_transcript_exon_variant	0.29	capreomycin	Uncertain significance
rrl	1474558	n.901G>A	non_coding_transcript_exon_variant	0.29	linezolid
rrl	1474582	n.925T>A	non_coding_transcript_exon_variant	0.43	capreomycin
rrl	1474582	n.925T>A	non_coding_transcript_exon_variant	0.43	linezolid
rrl	1474831	n.1174A>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1474831	n.1174A>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1474853	n.1196A>G	non_coding_transcript_exon_variant	0.46	capreomycin
rrl	1474853	n.1196A>G	non_coding_transcript_exon_variant	0.46	linezolid
rrl	1474864	n.1207C>T	non_coding_transcript_exon_variant	0.46	capreomycin	Not assoc w R
rrl	1474864	n.1207C>T	non_coding_transcript_exon_variant	0.46	linezolid	Uncertain significance
rrl	1475722	n.2065G>T	non_coding_transcript_exon_variant	0.72	capreomycin
rrl	1475722	n.2065G>T	non_coding_transcript_exon_variant	0.72	linezolid
rrl	1475747	n.2090A>G	non_coding_transcript_exon_variant	0.6	capreomycin	Uncertain significance
rrl	1475747	n.2090A>G	non_coding_transcript_exon_variant	0.6	linezolid	Uncertain significance
rrl	1475883	n.2226A>T	non_coding_transcript_exon_variant	0.47	capreomycin	Uncertain significance
rrl	1475883	n.2226A>T	non_coding_transcript_exon_variant	0.47	linezolid	Uncertain significance
rrl	1476130	n.2473G>A	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1476130	n.2473G>A	non_coding_transcript_exon_variant	0.64	linezolid	Uncertain significance
rrl	1476131	n.2474C>T	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1476131	n.2474C>T	non_coding_transcript_exon_variant	0.64	linezolid	Uncertain significance
rrl	1476141	n.2484A>G	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1476141	n.2484A>G	non_coding_transcript_exon_variant	0.67	linezolid	Uncertain significance
rrl	1476153	n.2496T>C	non_coding_transcript_exon_variant	0.69	capreomycin	Uncertain significance
rrl	1476153	n.2496T>C	non_coding_transcript_exon_variant	0.69	linezolid	Uncertain significance
rrl	1476164	n.2507A>G	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1476164	n.2507A>G	non_coding_transcript_exon_variant	0.71	linezolid	Uncertain significance
rrl	1476165	n.2508T>G	non_coding_transcript_exon_variant	0.71	capreomycin	Not assoc w R
rrl	1476165	n.2508T>G	non_coding_transcript_exon_variant	0.71	linezolid	Uncertain significance
rrl	1476194	n.2537A>G	non_coding_transcript_exon_variant	0.75	capreomycin	Not assoc w R
rrl	1476194	n.2537A>G	non_coding_transcript_exon_variant	0.75	linezolid	Uncertain significance
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.56	capreomycin	Not assoc w R
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.56	linezolid	Uncertain significance
rrl	1476201	n.2544C>T	non_coding_transcript_exon_variant	0.69	capreomycin	Not assoc w R
rrl	1476201	n.2544C>T	non_coding_transcript_exon_variant	0.69	linezolid	Uncertain significance
rrl	1476204	n.2547C>T	non_coding_transcript_exon_variant	0.75	capreomycin
rrl	1476204	n.2547C>T	non_coding_transcript_exon_variant	0.75	linezolid
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.58	linezolid	Uncertain significance
rrl	1476363	n.2706A>G	non_coding_transcript_exon_variant	0.61	capreomycin
rrl	1476363	n.2706A>G	non_coding_transcript_exon_variant	0.61	linezolid
rrl	1476366	n.2709A>C	non_coding_transcript_exon_variant	0.61	capreomycin
rrl	1476366	n.2709A>C	non_coding_transcript_exon_variant	0.61	linezolid
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.61	capreomycin	Uncertain significance
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.61	linezolid
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.64	linezolid	Uncertain significance
rrl	1476374	n.2717T>G	non_coding_transcript_exon_variant	0.64	capreomycin
rrl	1476374	n.2717T>G	non_coding_transcript_exon_variant	0.64	linezolid
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.68	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.68	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.56	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.56	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.59	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.59	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.59	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.59	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.52	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.52	linezolid	Uncertain significance
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R

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
capreomycin	rrs	n.1402C>A	Uncertain significance	Mutation from literature
kanamycin	rrs	n.1402C>A	Uncertain significance	Mutation from literature
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

TB-Profiler result