TB-Profiler

Lineage	Family	RDs	Frequency
lineage4.9	Euro-American (H37Rv-like)	None	0.85

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rrs	1472307	n.462C>T	non_coding_transcript_exon_variant	0.87	streptomycin	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
rpoC	763456	c.87A>G	synonymous_variant	0.69	rifampicin	Not assoc w R - Interim
rpoC	763468	c.99G>C	synonymous_variant	0.67	rifampicin	Not assoc w R - Interim
rpoC	763486	c.117T>C	synonymous_variant	0.67	rifampicin	Not assoc w R - Interim
rpoC	763528	c.159G>A	synonymous_variant	0.65	rifampicin	Not assoc w R - Interim
rpoC	763546	c.177A>G	synonymous_variant	0.59	rifampicin	Not assoc w R - Interim
rpoC	763570	c.201G>C	synonymous_variant	0.65	rifampicin	Not assoc w R - Interim
rpoC	763594	c.225C>T	synonymous_variant	0.56	rifampicin	Not assoc w R - Interim
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1471923	n.78T>C	non_coding_transcript_exon_variant	0.45	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1471934	n.89A>G	non_coding_transcript_exon_variant	0.48	streptomycin	Uncertain significance
					kanamycin
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1471969	n.124T>C	non_coding_transcript_exon_variant	0.55	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1471970	n.125G>A	non_coding_transcript_exon_variant	0.55	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472028	n.183A>T	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472030	n.185G>A	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472031	n.186G>A	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472034	n.189T>C	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472044	n.199G>C	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472053	n.211_212delGC	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472061	n.216A>T	non_coding_transcript_exon_variant	0.5	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472075	n.230A>G	non_coding_transcript_exon_variant	0.57	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472956	n.1111T>C	non_coding_transcript_exon_variant	0.22	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472957	n.1112C>T	non_coding_transcript_exon_variant	0.16	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472969	n.1124A>G	non_coding_transcript_exon_variant	0.54	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472970	n.1125C>G	non_coding_transcript_exon_variant	0.52	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472973	n.1128A>G	non_coding_transcript_exon_variant	0.16	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472977	n.1132G>C	non_coding_transcript_exon_variant	0.51	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472978	n.1133T>C	non_coding_transcript_exon_variant	0.53	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472990	n.1145A>G	non_coding_transcript_exon_variant	0.32	streptomycin	Uncertain significance
					kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472992	n.1147A>G	non_coding_transcript_exon_variant	0.17	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473005	n.1160C>T	non_coding_transcript_exon_variant	0.16	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473035	n.1190G>A	non_coding_transcript_exon_variant	0.17	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473055	n.1210C>T	non_coding_transcript_exon_variant	0.16	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473056	n.1211A>T	non_coding_transcript_exon_variant	0.17	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473066	n.1221A>G	non_coding_transcript_exon_variant	0.2	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473081	n.1236C>T	non_coding_transcript_exon_variant	0.16	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473088	n.1243A>G	non_coding_transcript_exon_variant	0.22	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473093	n.1248C>T	non_coding_transcript_exon_variant	0.21	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473104	n.1259C>T	non_coding_transcript_exon_variant	0.74	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473105	n.1260G>A	non_coding_transcript_exon_variant	0.44	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473111	n.1266A>G	non_coding_transcript_exon_variant	0.26	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473123	n.1278delAinsTT	non_coding_transcript_exon_variant	0.52	streptomycin
					kanamycin
					capreomycin
					amikacin
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	1473166	n.1321G>A	non_coding_transcript_exon_variant	0.61	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1474051	n.394T>C	non_coding_transcript_exon_variant	0.8	capreomycin
rrl	1474051	n.394T>C	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1474054	n.397T>C	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1474054	n.397T>C	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1474056	n.399T>C	non_coding_transcript_exon_variant	0.8	capreomycin
rrl	1474056	n.399T>C	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1474103	n.446A>T	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1474103	n.446A>T	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1474104	n.447G>A	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1474104	n.447G>A	non_coding_transcript_exon_variant	0.67	linezolid	Uncertain significance
rrl	1474111	n.454T>C	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1474111	n.454T>C	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1474112	n.455T>A	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1474112	n.455T>A	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1474140	n.483C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1474140	n.483C>T	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1474151	n.494C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1474151	n.494C>T	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1474181	n.524C>T	non_coding_transcript_exon_variant	0.81	capreomycin	Uncertain significance
rrl	1474181	n.524C>T	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1474249	n.592G>T	non_coding_transcript_exon_variant	0.86	capreomycin	Uncertain significance
rrl	1474249	n.592G>T	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1474291	n.634_649delTTTCCTCTCCGGAGGAinsC	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1474291	n.634_649delTTTCCTCTCCGGAGGAinsC	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1474308	n.651G>T	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1474308	n.651G>T	non_coding_transcript_exon_variant	0.7	linezolid	Uncertain significance
rrl	1474310	n.653T>G	non_coding_transcript_exon_variant	0.64	capreomycin
rrl	1474310	n.653T>G	non_coding_transcript_exon_variant	0.64	linezolid
rrl	1474356	n.699T>C	non_coding_transcript_exon_variant	0.73	capreomycin	Uncertain significance
rrl	1474356	n.699T>C	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1474376	n.719T>C	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1474376	n.719T>C	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1474639	n.982G>A	non_coding_transcript_exon_variant	0.6	capreomycin	Uncertain significance
rrl	1474639	n.982G>A	non_coding_transcript_exon_variant	0.6	linezolid	Uncertain significance
rrl	1475199	n.1542G>A	non_coding_transcript_exon_variant	0.8	capreomycin
rrl	1475199	n.1542G>A	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475206	n.1549C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475206	n.1549C>T	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475209	n.1552G>C	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475209	n.1552G>C	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475213	n.1556C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475213	n.1556C>T	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1475881	n.2224T>C	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1475881	n.2224T>C	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.72	capreomycin	Not assoc w R
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.72	linezolid	Uncertain significance
rrl	1476025	n.2368G>T	non_coding_transcript_exon_variant	0.68	capreomycin
rrl	1476025	n.2368G>T	non_coding_transcript_exon_variant	0.68	linezolid
rrl	1476030	n.2373A>G	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1476030	n.2373A>G	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1476032	n.2375C>A	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1476032	n.2375C>A	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1476033	n.2376T>C	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1476033	n.2376T>C	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1476034	n.2377C>A	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1476034	n.2377C>A	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1476045	n.2388G>T	non_coding_transcript_exon_variant	0.73	capreomycin	Uncertain significance
rrl	1476045	n.2388G>T	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1476047	n.2390G>T	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1476047	n.2390G>T	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1476049	n.2392C>T	non_coding_transcript_exon_variant	0.73	capreomycin	Uncertain significance
rrl	1476049	n.2392C>T	non_coding_transcript_exon_variant	0.73	linezolid	Uncertain significance
rrl	1476086	n.2429G>A	non_coding_transcript_exon_variant	0.76	capreomycin	Uncertain significance
rrl	1476086	n.2429G>A	non_coding_transcript_exon_variant	0.76	linezolid	Uncertain significance
rrl	1476089	n.2432T>C	non_coding_transcript_exon_variant	0.76	capreomycin
rrl	1476089	n.2432T>C	non_coding_transcript_exon_variant	0.76	linezolid
rrl	1476095	n.2438C>G	non_coding_transcript_exon_variant	0.81	capreomycin
rrl	1476095	n.2438C>G	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1476105	n.2448_2449delGAinsT	non_coding_transcript_exon_variant	0.79	capreomycin
rrl	1476105	n.2448_2449delGAinsT	non_coding_transcript_exon_variant	0.79	linezolid
rrl	1476115	n.2458T>C	non_coding_transcript_exon_variant	0.79	capreomycin	Uncertain significance
rrl	1476115	n.2458T>C	non_coding_transcript_exon_variant	0.79	linezolid	Uncertain significance
rrl	1476117	n.2460G>C	non_coding_transcript_exon_variant	0.79	capreomycin
rrl	1476117	n.2460G>C	non_coding_transcript_exon_variant	0.79	linezolid
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.86	capreomycin	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.77	capreomycin	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.77	linezolid	Uncertain significance
rrl	1476295	n.2638C>G	non_coding_transcript_exon_variant	0.26	capreomycin	Uncertain significance
rrl	1476295	n.2638C>G	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1476296	n.2639C>T	non_coding_transcript_exon_variant	0.26	capreomycin	Uncertain significance
rrl	1476296	n.2639C>T	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1476301	n.2644A>T	non_coding_transcript_exon_variant	0.27	capreomycin	Uncertain significance
rrl	1476301	n.2644A>T	non_coding_transcript_exon_variant	0.27	linezolid	Uncertain significance
rrl	1476311	n.2654G>C	non_coding_transcript_exon_variant	0.27	capreomycin	Uncertain significance
rrl	1476311	n.2654G>C	non_coding_transcript_exon_variant	0.27	linezolid	Uncertain significance
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.26	capreomycin	Uncertain significance
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.27	capreomycin	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.27	linezolid	Uncertain significance
rrl	1476353	n.2696G>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476353	n.2696G>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.17	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.17	linezolid	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.39	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.39	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.32	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.32	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.16	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.16	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.3	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.3	linezolid	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.29	capreomycin	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.29	linezolid	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.59	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.59	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.44	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.44	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.33	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.26	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1476583	n.2926G>A	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476583	n.2926G>A	non_coding_transcript_exon_variant	0.58	linezolid
rrl	1476584	n.2927C>T	non_coding_transcript_exon_variant	0.58	capreomycin	Not assoc w R
rrl	1476584	n.2927C>T	non_coding_transcript_exon_variant	0.58	linezolid	Uncertain significance
rrl	1476597	n.2940G>A	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476597	n.2940G>A	non_coding_transcript_exon_variant	0.58	linezolid
rrl	1476608	n.2951C>G	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476608	n.2951C>G	non_coding_transcript_exon_variant	0.58	linezolid	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	rrs	n.462C>T	Uncertain significance	Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

TB-Profiler result