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	0.31	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
rrs	1472127	n.282C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472128	n.283G>C	non_coding_transcript_exon_variant	0.8	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472129	n.284G>A	non_coding_transcript_exon_variant	0.86	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472150	n.305T>G	non_coding_transcript_exon_variant	0.95	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472151	n.306C>A	non_coding_transcript_exon_variant	0.79	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472160	n.315C>T	non_coding_transcript_exon_variant	0.88	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.93	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472181	n.336G>A	non_coding_transcript_exon_variant	0.43	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472210	n.365A>C	non_coding_transcript_exon_variant	0.39	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472215	n.370A>G	non_coding_transcript_exon_variant	0.47	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472223	n.378C>G	non_coding_transcript_exon_variant	0.34	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472225	n.380C>A	non_coding_transcript_exon_variant	0.94	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472228	n.383G>C	non_coding_transcript_exon_variant	0.33	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472234	n.389T>C	non_coding_transcript_exon_variant	0.6	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472251	n.406G>C	non_coding_transcript_exon_variant	0.93	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472338	n.493A>C	non_coding_transcript_exon_variant	0.81	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472344	n.499C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472379	n.534T>G	non_coding_transcript_exon_variant	0.91	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472382	n.537G>A	non_coding_transcript_exon_variant	0.58	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472389	n.544G>A	non_coding_transcript_exon_variant	0.83	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472396	n.551A>T	non_coding_transcript_exon_variant	0.69	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472400	n.555C>T	non_coding_transcript_exon_variant	0.42	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472405	n.560C>T	non_coding_transcript_exon_variant	0.48	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472545	n.700A>G	non_coding_transcript_exon_variant	0.83	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472549	n.704G>A	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472557	n.712G>A	non_coding_transcript_exon_variant	0.37	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472579	n.734G>A	non_coding_transcript_exon_variant	0.43	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472581	n.736A>C	non_coding_transcript_exon_variant	0.81	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472582	n.737G>A	non_coding_transcript_exon_variant	0.46	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472584	n.739A>C	non_coding_transcript_exon_variant	0.38	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472598	n.753A>C	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472599	n.754G>T	non_coding_transcript_exon_variant	0.5	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472616	n.771G>A	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472647	n.802C>T	non_coding_transcript_exon_variant	0.37	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472655	n.810G>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472697	n.852T>C	non_coding_transcript_exon_variant	0.93	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472714	n.869A>G	non_coding_transcript_exon_variant	0.5	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472715	n.870C>T	non_coding_transcript_exon_variant	0.77	kanamycin
					amikacin
					streptomycin
					capreomycin
rrs	1472734	n.889C>T	non_coding_transcript_exon_variant	0.39	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472742	n.897C>T	non_coding_transcript_exon_variant	0.35	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472744	n.899A>G	non_coding_transcript_exon_variant	0.59	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472767	n.922G>A	non_coding_transcript_exon_variant	0.37	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472779	n.934G>A	non_coding_transcript_exon_variant	0.41	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472781	n.936C>T	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472793	n.948A>C	non_coding_transcript_exon_variant	0.39	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472793	n.948A>T	non_coding_transcript_exon_variant	0.55	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Not assoc w R
rrs	1472803	n.958T>A	non_coding_transcript_exon_variant	0.97	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1472895	n.1050C>T	non_coding_transcript_exon_variant	0.78	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473026	n.1181T>C	non_coding_transcript_exon_variant	0.48	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473035	n.1190G>A	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473053	n.1208T>A	non_coding_transcript_exon_variant	0.4	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473056	n.1211A>T	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473062	n.1217T>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473068	n.1223A>G	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473084	n.1239T>C	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin
rrs	1473179	n.1334C>T	non_coding_transcript_exon_variant	0.58	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473192	n.1347A>G	non_coding_transcript_exon_variant	0.88	kanamycin	Uncertain significance
					amikacin	Not assoc w R
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473199	n.1356delA	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473205	n.1360T>C	non_coding_transcript_exon_variant	0.9	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
					capreomycin	Uncertain significance
rrs	1473215	n.1370A>G	non_coding_transcript_exon_variant	0.32	kanamycin
					amikacin
					streptomycin	Uncertain significance
					capreomycin
rrl	1474197	n.540C>A	non_coding_transcript_exon_variant	0.43	capreomycin
rrl	1474197	n.540C>A	non_coding_transcript_exon_variant	0.43	linezolid
rrl	1474208	n.551C>T	non_coding_transcript_exon_variant	0.57	capreomycin
rrl	1474208	n.551C>T	non_coding_transcript_exon_variant	0.57	linezolid
rrl	1474213	n.556G>A	non_coding_transcript_exon_variant	0.59	capreomycin
rrl	1474213	n.556G>A	non_coding_transcript_exon_variant	0.59	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	0.88	capreomycin
rrl	1474228	n.571T>G	non_coding_transcript_exon_variant	0.88	linezolid
rrl	1474252	n.595T>A	non_coding_transcript_exon_variant	0.76	capreomycin	Uncertain significance
rrl	1474252	n.595T>A	non_coding_transcript_exon_variant	0.76	linezolid	Uncertain significance
rrl	1474476	n.819C>T	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1474476	n.819C>T	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1474483	n.826C>G	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1474483	n.826C>G	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1474488	n.831G>C	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1474488	n.831G>C	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1474496	n.839C>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1474496	n.839C>G	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1474507	n.850G>C	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1474507	n.850G>C	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1474516	n.859C>G	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1474516	n.859C>G	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1474537	n.880G>A	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1474537	n.880G>A	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1474551	n.894G>C	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1474551	n.894G>C	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1474558	n.901G>A	non_coding_transcript_exon_variant	0.72	capreomycin	Uncertain significance
rrl	1474558	n.901G>A	non_coding_transcript_exon_variant	0.72	linezolid
rrl	1474582	n.925T>C	non_coding_transcript_exon_variant	0.48	capreomycin	Uncertain significance
rrl	1474582	n.925T>C	non_coding_transcript_exon_variant	0.48	linezolid	Uncertain significance
rrl	1474584	n.927C>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1474584	n.927C>G	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1474586	n.929T>A	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1474586	n.929T>A	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1474591	n.934G>T	non_coding_transcript_exon_variant	0.41	capreomycin
rrl	1474591	n.934G>T	non_coding_transcript_exon_variant	0.41	linezolid
rrl	1474594	n.937G>C	non_coding_transcript_exon_variant	0.78	capreomycin
rrl	1474594	n.937G>C	non_coding_transcript_exon_variant	0.78	linezolid
rrl	1474597	n.940T>A	non_coding_transcript_exon_variant	0.38	capreomycin
rrl	1474597	n.940T>A	non_coding_transcript_exon_variant	0.38	linezolid
rrl	1474777	n.1120T>C	non_coding_transcript_exon_variant	0.91	capreomycin	Not assoc w R
rrl	1474777	n.1120T>C	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1474812	n.1155G>C	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1474812	n.1155G>C	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1474839	n.1182C>T	non_coding_transcript_exon_variant	0.55	capreomycin	Uncertain significance
rrl	1474839	n.1182C>T	non_coding_transcript_exon_variant	0.55	linezolid	Uncertain significance
rrl	1474844	n.1187G>T	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1474844	n.1187G>T	non_coding_transcript_exon_variant	0.67	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	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	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.81	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.47	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.47	linezolid	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.88	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.88	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.4	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.4	linezolid	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1476383	n.2726T>A	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.7	linezolid	Uncertain significance
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.42	capreomycin
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.42	linezolid
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.56	capreomycin
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.56	linezolid
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.61	capreomycin
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.61	linezolid
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.43	capreomycin
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.43	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.79	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.79	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

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
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

TB-Profiler result