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	0.43	streptomycin	Uncertain significance	Mutation from literature
rrs	1473247	n.1402C>A	non_coding_transcript_exon_variant	0.5	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	1472150	n.305T>A	non_coding_transcript_exon_variant	0.56	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472150	n.305T>G	non_coding_transcript_exon_variant	0.44	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472151	n.306C>A	non_coding_transcript_exon_variant	0.87	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472160	n.315C>T	non_coding_transcript_exon_variant	0.96	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.85	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472181	n.336G>A	non_coding_transcript_exon_variant	0.52	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472207	n.362A>G	non_coding_transcript_exon_variant	0.24	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472214	n.369C>G	non_coding_transcript_exon_variant	0.5	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472215	n.370A>G	non_coding_transcript_exon_variant	0.33	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472223	n.378C>G	non_coding_transcript_exon_variant	0.48	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472225	n.380C>A	non_coding_transcript_exon_variant	0.89	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Uncertain significance
rrs	1472228	n.383G>C	non_coding_transcript_exon_variant	0.48	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472234	n.389T>A	non_coding_transcript_exon_variant	0.42	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472235	n.390G>C	non_coding_transcript_exon_variant	0.57	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472240	n.395G>A	non_coding_transcript_exon_variant	0.71	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472242	n.397C>A	non_coding_transcript_exon_variant	0.37	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472244	n.399C>T	non_coding_transcript_exon_variant	0.33	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472251	n.406G>A	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472256	n.411T>A	non_coding_transcript_exon_variant	0.82	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472264	n.419_420delTTinsCTA	non_coding_transcript_exon_variant	0.7	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472537	n.692C>T	non_coding_transcript_exon_variant	0.73	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472544	n.699C>T	non_coding_transcript_exon_variant	0.76	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472549	n.704G>A	non_coding_transcript_exon_variant	0.35	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472557	n.712G>A	non_coding_transcript_exon_variant	0.83	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472571	n.726G>C	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472573	n.728C>T	non_coding_transcript_exon_variant	0.58	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472579	n.734G>A	non_coding_transcript_exon_variant	0.8	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472581	n.736A>T	non_coding_transcript_exon_variant	0.94	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472583	n.738T>C	non_coding_transcript_exon_variant	0.25	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472592	n.747C>T	non_coding_transcript_exon_variant	0.43	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472598	n.753A>C	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472599	n.754G>T	non_coding_transcript_exon_variant	0.68	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472606	n.761C>T	non_coding_transcript_exon_variant	0.32	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472616	n.771G>A	non_coding_transcript_exon_variant	0.73	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472713	n.868T>C	non_coding_transcript_exon_variant	0.33	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472715	n.870C>T	non_coding_transcript_exon_variant	0.65	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472716	n.871C>T	non_coding_transcript_exon_variant	0.5	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472719	n.874G>A	non_coding_transcript_exon_variant	0.73	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472733	n.888G>C	non_coding_transcript_exon_variant	0.33	streptomycin	Uncertain significance
					kanamycin
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472735	n.890C>G	non_coding_transcript_exon_variant	0.27	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472740	n.895G>C	non_coding_transcript_exon_variant	0.25	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472742	n.897C>T	non_coding_transcript_exon_variant	0.79	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472744	n.899A>G	non_coding_transcript_exon_variant	0.96	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472781	n.936C>T	non_coding_transcript_exon_variant	0.95	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472793	n.948A>T	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472803	n.958T>A	non_coding_transcript_exon_variant	0.69	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472813	n.968A>G	non_coding_transcript_exon_variant	0.29	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473145	n.1300C>T	non_coding_transcript_exon_variant	0.79	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473148	n.1303G>A	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473163	n.1318C>T	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473166	n.1321G>A	non_coding_transcript_exon_variant	0.8	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473172	n.1327T>C	non_coding_transcript_exon_variant	0.89	streptomycin	Not assoc w R
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1473173	n.1328C>T	non_coding_transcript_exon_variant	0.89	streptomycin	Not assoc w R
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1473177	n.1332G>T	non_coding_transcript_exon_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473192	n.1347A>G	non_coding_transcript_exon_variant	0.91	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473193	n.1348G>C	non_coding_transcript_exon_variant	0.78	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473204	n.1359C>G	non_coding_transcript_exon_variant	0.78	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473205	n.1360T>C	non_coding_transcript_exon_variant	0.91	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473248	n.1403G>A	non_coding_transcript_exon_variant	0.6	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473249	n.1404T>C	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1474839	n.1182C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1474839	n.1182C>T	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1474844	n.1187G>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1474844	n.1187G>T	non_coding_transcript_exon_variant	0.82	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	1475858	n.2201T>C	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1475858	n.2201T>C	non_coding_transcript_exon_variant	0.67	linezolid	Uncertain significance
rrl	1475866	n.2209T>A	non_coding_transcript_exon_variant	0.64	capreomycin	Uncertain significance
rrl	1475866	n.2209T>A	non_coding_transcript_exon_variant	0.64	linezolid	Uncertain significance
rrl	1476312	n.2655T>C	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476312	n.2655T>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1476322	n.2665C>A	non_coding_transcript_exon_variant	0.42	capreomycin
rrl	1476322	n.2665C>A	non_coding_transcript_exon_variant	0.42	linezolid
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.5	capreomycin	Uncertain significance
rrl	1476332	n.2675G>C	non_coding_transcript_exon_variant	0.5	linezolid	Uncertain significance
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.5	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.5	linezolid
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.41	capreomycin	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.41	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	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.59	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.59	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.97	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.97	linezolid	Uncertain significance
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.66	capreomycin
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.66	linezolid
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.47	capreomycin	Uncertain significance
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.47	linezolid
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.87	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.87	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.51	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.51	linezolid	Uncertain significance
rrl	1476381	n.2724G>A	non_coding_transcript_exon_variant	0.63	capreomycin
rrl	1476381	n.2724G>A	non_coding_transcript_exon_variant	0.63	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	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.35	capreomycin	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.35	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.55	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.55	linezolid
rrl	1476417	n.2760T>C	non_coding_transcript_exon_variant	0.51	capreomycin	Uncertain significance
rrl	1476417	n.2760T>C	non_coding_transcript_exon_variant	0.51	linezolid
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.5	capreomycin
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.5	linezolid
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.41	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.41	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.28	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.28	linezolid	Uncertain significance
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.52	capreomycin
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.52	linezolid
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.51	capreomycin
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.51	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.6	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.6	linezolid
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	0.59	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.59	linezolid	Uncertain significance
rrl	1476519	n.2862C>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476519	n.2862C>G	non_coding_transcript_exon_variant	1.0	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