TB-Profiler

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	1.0

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rrs	1472733	n.888G>A	non_coding_transcript_exon_variant	0.65	streptomycin	Uncertain significance	Mutation from literature
rrs	1473247	n.1402C>A	non_coding_transcript_exon_variant	0.41	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
rrs	1472127	n.282C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472128	n.283G>C	non_coding_transcript_exon_variant	0.89	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472129	n.284G>A	non_coding_transcript_exon_variant	0.94	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472138	n.293C>A	non_coding_transcript_exon_variant	0.46	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472147	n.302G>T	non_coding_transcript_exon_variant	0.39	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472151	n.306C>A	non_coding_transcript_exon_variant	0.87	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472160	n.315C>T	non_coding_transcript_exon_variant	0.98	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472181	n.336G>A	non_coding_transcript_exon_variant	0.36	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472223	n.378C>G	non_coding_transcript_exon_variant	0.63	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472225	n.380C>A	non_coding_transcript_exon_variant	0.92	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472228	n.383G>C	non_coding_transcript_exon_variant	0.68	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472240	n.395G>A	non_coding_transcript_exon_variant	0.76	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472251	n.406G>A	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472537	n.692C>T	non_coding_transcript_exon_variant	0.94	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472544	n.699C>T	non_coding_transcript_exon_variant	0.81	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472557	n.712G>A	non_coding_transcript_exon_variant	0.89	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472571	n.726G>C	non_coding_transcript_exon_variant	0.97	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472573	n.728C>T	non_coding_transcript_exon_variant	0.68	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472574	n.729T>A	non_coding_transcript_exon_variant	0.37	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472579	n.734G>A	non_coding_transcript_exon_variant	0.88	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472581	n.736A>T	non_coding_transcript_exon_variant	0.85	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472592	n.747C>T	non_coding_transcript_exon_variant	0.35	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472598	n.753A>C	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472599	n.754G>T	non_coding_transcript_exon_variant	0.68	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472616	n.771G>A	non_coding_transcript_exon_variant	0.82	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472713	n.868T>C	non_coding_transcript_exon_variant	0.37	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472715	n.870C>T	non_coding_transcript_exon_variant	0.65	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472716	n.871C>T	non_coding_transcript_exon_variant	0.59	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472719	n.874G>A	non_coding_transcript_exon_variant	0.6	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472734	n.889C>T	non_coding_transcript_exon_variant	0.3	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472742	n.897C>T	non_coding_transcript_exon_variant	0.95	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472744	n.899A>G	non_coding_transcript_exon_variant	0.92	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472779	n.934G>A	non_coding_transcript_exon_variant	0.35	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472781	n.936C>T	non_coding_transcript_exon_variant	0.91	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472786	n.941C>T	non_coding_transcript_exon_variant	0.33	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472793	n.948A>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472803	n.958T>A	non_coding_transcript_exon_variant	0.73	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472805	n.960C>A	non_coding_transcript_exon_variant	0.29	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472806	n.961A>T	non_coding_transcript_exon_variant	0.29	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472813	n.968A>G	non_coding_transcript_exon_variant	0.28	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472824	n.979T>A	non_coding_transcript_exon_variant	0.83	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473145	n.1300C>T	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473148	n.1303G>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473158	n.1313T>C	non_coding_transcript_exon_variant	0.53	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473163	n.1318C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473166	n.1321G>A	non_coding_transcript_exon_variant	0.64	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473172	n.1327T>C	non_coding_transcript_exon_variant	0.91	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1473173	n.1328C>T	non_coding_transcript_exon_variant	0.91	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1473177	n.1332G>T	non_coding_transcript_exon_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473192	n.1347A>G	non_coding_transcript_exon_variant	0.97	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473193	n.1348G>C	non_coding_transcript_exon_variant	0.79	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473200	n.1355_1357delAACinsCAT	non_coding_transcript_exon_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473204	n.1359C>G	non_coding_transcript_exon_variant	0.78	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473205	n.1360T>C	non_coding_transcript_exon_variant	0.97	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473248	n.1403G>A	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473249	n.1404T>C	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473255	n.1410A>G	non_coding_transcript_exon_variant	0.83	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1474171	n.514C>G	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1474171	n.514C>G	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1474181	n.524C>A	non_coding_transcript_exon_variant	0.82	capreomycin
rrl	1474181	n.524C>A	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1474184	n.527C>T	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1474184	n.527C>T	non_coding_transcript_exon_variant	0.64	linezolid	Uncertain significance
rrl	1474186	n.529A>G	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1474186	n.529A>G	non_coding_transcript_exon_variant	0.67	linezolid	Uncertain significance
rrl	1474202	n.545T>A	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1474202	n.545T>A	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1474218	n.561T>A	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1474218	n.561T>A	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1474228	n.571T>G	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1474228	n.571T>G	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1475783	n.2126T>G	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1475783	n.2126T>G	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance
rrl	1475803	n.2146T>C	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1475803	n.2146T>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1475804	n.2147G>C	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1475804	n.2147G>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1475816	n.2159C>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1475816	n.2159C>G	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1475817	n.2160A>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1475817	n.2160A>G	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1476322	n.2665C>A	non_coding_transcript_exon_variant	0.59	capreomycin
rrl	1476322	n.2665C>A	non_coding_transcript_exon_variant	0.59	linezolid
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.36	capreomycin	Uncertain significance
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.36	linezolid	Uncertain significance
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.61	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.61	linezolid
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.3	capreomycin	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.3	linezolid	Uncertain significance
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.98	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.98	linezolid	Uncertain significance
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.51	capreomycin	Uncertain significance
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.51	linezolid
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.9	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.9	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.42	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.42	linezolid	Uncertain significance
rrl	1476381	n.2724G>A	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1476381	n.2724G>A	non_coding_transcript_exon_variant	0.7	linezolid
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.98	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.98	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.59	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.59	linezolid
rrl	1476417	n.2760T>C	non_coding_transcript_exon_variant	0.54	capreomycin	Uncertain significance
rrl	1476417	n.2760T>C	non_coding_transcript_exon_variant	0.54	linezolid
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.26	capreomycin	Uncertain significance
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.55	capreomycin
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.55	linezolid
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.34	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.34	linezolid	Uncertain significance
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.53	capreomycin
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.53	linezolid
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.54	capreomycin
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.54	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.59	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.59	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.28	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.28	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.56	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.56	linezolid	Uncertain significance
rrl	1476514	n.2857C>T	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1476514	n.2857C>T	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin	rrs	n.888G>A	Uncertain significance	Mutation from literature
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