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	1472644	n.799C>T	non_coding_transcript_exon_variant	0.21	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
gyrA	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	moxifloxacin	Not assoc w R
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	0.96	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.94	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472251	n.406G>A	non_coding_transcript_exon_variant	0.96	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472282	n.437T>G	non_coding_transcript_exon_variant	0.83	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472284	n.439C>T	non_coding_transcript_exon_variant	0.82	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472286	n.441C>G	non_coding_transcript_exon_variant	0.84	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472293	n.448C>A	non_coding_transcript_exon_variant	0.84	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472297	n.453_465delGTCCGGGTTCTCT	non_coding_transcript_exon_variant	0.85	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472313	n.468delGinsAA	non_coding_transcript_exon_variant	0.84	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472315	n.470T>G	non_coding_transcript_exon_variant	0.82	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472328	n.483G>C	non_coding_transcript_exon_variant	0.86	kanamycin
					capreomycin
					streptomycin	Uncertain significance
					amikacin
rrs	1472332	n.487A>G	non_coding_transcript_exon_variant	0.86	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472333	n.488G>A	non_coding_transcript_exon_variant	0.87	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472338	n.493A>G	non_coding_transcript_exon_variant	0.88	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472344	n.499C>T	non_coding_transcript_exon_variant	0.87	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472379	n.534T>C	non_coding_transcript_exon_variant	0.84	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472400	n.555C>T	non_coding_transcript_exon_variant	0.71	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472416	n.571C>T	non_coding_transcript_exon_variant	0.53	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472422	n.577T>C	non_coding_transcript_exon_variant	0.46	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472427	n.582T>G	non_coding_transcript_exon_variant	0.25	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472435	n.590T>C	non_coding_transcript_exon_variant	0.25	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472476	n.631A>G	non_coding_transcript_exon_variant	0.5	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472494	n.649A>G	non_coding_transcript_exon_variant	0.8	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472496	n.651T>A	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472498	n.653C>T	non_coding_transcript_exon_variant	0.82	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472581	n.736A>C	non_coding_transcript_exon_variant	0.61	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472581	n.736A>T	non_coding_transcript_exon_variant	0.25	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472584	n.739A>T	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472597	n.752G>A	non_coding_transcript_exon_variant	0.22	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472607	n.762G>A	non_coding_transcript_exon_variant	0.22	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472647	n.802C>T	non_coding_transcript_exon_variant	0.46	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472655	n.810G>T	non_coding_transcript_exon_variant	0.8	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472660	n.815T>C	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472673	n.828_837delTTTCCTTCCTinsGGCCACCCG	non_coding_transcript_exon_variant	0.6	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472686	n.841_842delGAinsTT	non_coding_transcript_exon_variant	0.58	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472690	n.845C>T	non_coding_transcript_exon_variant	0.37	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin
rrs	1472692	n.847T>C	non_coding_transcript_exon_variant	0.72	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472707	n.862A>T	non_coding_transcript_exon_variant	0.38	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472714	n.869A>G	non_coding_transcript_exon_variant	0.72	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472790	n.945T>C	non_coding_transcript_exon_variant	0.19	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472824	n.979T>A	non_coding_transcript_exon_variant	0.18	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472828	n.983T>C	non_coding_transcript_exon_variant	0.16	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472910	n.1065G>A	non_coding_transcript_exon_variant	0.19	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472954	n.1109T>C	non_coding_transcript_exon_variant	0.15	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472992	n.1147A>G	non_coding_transcript_exon_variant	0.14	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473035	n.1190G>A	non_coding_transcript_exon_variant	0.19	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473055	n.1210C>T	non_coding_transcript_exon_variant	0.18	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473056	n.1211A>T	non_coding_transcript_exon_variant	0.18	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473066	n.1221A>G	non_coding_transcript_exon_variant	0.18	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1475943	n.2286G>A	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1475943	n.2286G>A	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1475945	n.2288C>A	non_coding_transcript_exon_variant	0.3	capreomycin
rrl	1475945	n.2288C>A	non_coding_transcript_exon_variant	0.3	linezolid
rrl	1475952	n.2295A>G	non_coding_transcript_exon_variant	0.32	capreomycin	Uncertain significance
rrl	1475952	n.2295A>G	non_coding_transcript_exon_variant	0.32	linezolid	Uncertain significance
rrl	1475970	n.2313C>T	non_coding_transcript_exon_variant	0.23	capreomycin	Uncertain significance
rrl	1475970	n.2313C>T	non_coding_transcript_exon_variant	0.23	linezolid	Uncertain significance
rrl	1475977	n.2320A>G	non_coding_transcript_exon_variant	0.2	capreomycin	Uncertain significance
rrl	1475977	n.2320A>G	non_coding_transcript_exon_variant	0.2	linezolid	Uncertain significance
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.16	capreomycin	Not assoc w R
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.16	linezolid	Uncertain significance
rrl	1476131	n.2474C>T	non_coding_transcript_exon_variant	0.29	capreomycin	Uncertain significance
rrl	1476131	n.2474C>T	non_coding_transcript_exon_variant	0.29	linezolid	Uncertain significance
rrl	1476164	n.2507A>G	non_coding_transcript_exon_variant	0.35	capreomycin	Uncertain significance
rrl	1476164	n.2507A>G	non_coding_transcript_exon_variant	0.35	linezolid	Uncertain significance
rrl	1476179	n.2522C>T	non_coding_transcript_exon_variant	0.38	capreomycin
rrl	1476179	n.2522C>T	non_coding_transcript_exon_variant	0.38	linezolid
rrl	1476194	n.2537A>G	non_coding_transcript_exon_variant	0.35	capreomycin	Not assoc w R
rrl	1476194	n.2537A>G	non_coding_transcript_exon_variant	0.35	linezolid	Uncertain significance
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.37	capreomycin	Not assoc w R
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.37	linezolid	Uncertain significance
rrl	1476204	n.2547C>T	non_coding_transcript_exon_variant	0.21	capreomycin
rrl	1476204	n.2547C>T	non_coding_transcript_exon_variant	0.21	linezolid
rrl	1476207	n.2550T>C	non_coding_transcript_exon_variant	0.3	capreomycin
rrl	1476207	n.2550T>C	non_coding_transcript_exon_variant	0.3	linezolid
rrl	1476214	n.2557G>T	non_coding_transcript_exon_variant	0.34	capreomycin	Uncertain significance
rrl	1476214	n.2557G>T	non_coding_transcript_exon_variant	0.34	linezolid	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.4	capreomycin	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.4	linezolid	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.28	capreomycin	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.28	linezolid	Uncertain significance
rrl	1476252	n.2595T>G	non_coding_transcript_exon_variant	0.32	capreomycin	Uncertain significance
rrl	1476252	n.2595T>G	non_coding_transcript_exon_variant	0.32	linezolid	Uncertain significance
rrl	1476255	n.2598A>G	non_coding_transcript_exon_variant	0.16	capreomycin	Uncertain significance
rrl	1476255	n.2598A>G	non_coding_transcript_exon_variant	0.16	linezolid
rrl	1476256	n.2599A>G	non_coding_transcript_exon_variant	0.3	capreomycin	Uncertain significance
rrl	1476256	n.2599A>G	non_coding_transcript_exon_variant	0.3	linezolid	Uncertain significance
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.29	capreomycin	Not assoc w R
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.29	linezolid	Uncertain significance
rrl	1476267	n.2610G>T	non_coding_transcript_exon_variant	0.24	capreomycin
rrl	1476267	n.2610G>T	non_coding_transcript_exon_variant	0.24	linezolid
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.24	capreomycin	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.24	linezolid	Uncertain significance
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin	rrs	n.799C>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