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	0.7	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	0.99	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	0.99	moxifloxacin	Not assoc w R
rrs	1472119	n.274G>A	non_coding_transcript_exon_variant	0.58	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	0.96	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.97	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472251	n.406G>A	non_coding_transcript_exon_variant	0.94	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472282	n.437T>G	non_coding_transcript_exon_variant	0.35	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472284	n.439C>T	non_coding_transcript_exon_variant	0.32	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472285	n.440A>G	non_coding_transcript_exon_variant	0.14	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472286	n.441C>G	non_coding_transcript_exon_variant	0.4	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472289	n.444T>G	non_coding_transcript_exon_variant	0.21	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472290	n.445C>G	non_coding_transcript_exon_variant	0.21	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472293	n.448C>A	non_coding_transcript_exon_variant	0.34	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472297	n.453_465delGTCCGGGTTCTCT	non_coding_transcript_exon_variant	0.36	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472313	n.468_470delGATinsAAAG	non_coding_transcript_exon_variant	0.35	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472324	n.479G>C	non_coding_transcript_exon_variant	0.25	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472325	n.480G>C	non_coding_transcript_exon_variant	0.25	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472328	n.483G>C	non_coding_transcript_exon_variant	0.5	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472330	n.485G>T	non_coding_transcript_exon_variant	0.16	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472332	n.487A>G	non_coding_transcript_exon_variant	0.43	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472333	n.488G>A	non_coding_transcript_exon_variant	0.42	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472338	n.493A>G	non_coding_transcript_exon_variant	0.45	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472344	n.499C>T	non_coding_transcript_exon_variant	0.72	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472379	n.534T>C	non_coding_transcript_exon_variant	0.49	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472400	n.555C>T	non_coding_transcript_exon_variant	0.36	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472416	n.571C>T	non_coding_transcript_exon_variant	0.24	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472422	n.577T>C	non_coding_transcript_exon_variant	0.16	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Uncertain significance
rrs	1472435	n.590T>C	non_coding_transcript_exon_variant	0.65	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472438	n.593T>C	non_coding_transcript_exon_variant	0.65	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472439	n.594C>T	non_coding_transcript_exon_variant	0.63	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472447	n.602C>T	non_coding_transcript_exon_variant	0.64	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472448	n.603T>C	non_coding_transcript_exon_variant	0.67	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472450	n.605A>G	non_coding_transcript_exon_variant	0.67	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472451	n.606C>G	non_coding_transcript_exon_variant	0.66	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472461	n.616G>C	non_coding_transcript_exon_variant	0.65	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472462	n.617T>C	non_coding_transcript_exon_variant	0.67	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472464	n.619A>G	non_coding_transcript_exon_variant	0.69	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472471	n.626G>A	non_coding_transcript_exon_variant	0.67	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472485	n.640delGinsTA	non_coding_transcript_exon_variant	0.41	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472489	n.644A>T	non_coding_transcript_exon_variant	0.38	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472494	n.649A>G	non_coding_transcript_exon_variant	0.82	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472496	n.651T>A	non_coding_transcript_exon_variant	0.44	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472498	n.653C>T	non_coding_transcript_exon_variant	0.85	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472569	n.724G>A	non_coding_transcript_exon_variant	0.81	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472581	n.736A>T	non_coding_transcript_exon_variant	0.85	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1472597	n.752G>A	non_coding_transcript_exon_variant	0.77	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472607	n.762G>A	non_coding_transcript_exon_variant	0.75	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472655	n.810G>T	non_coding_transcript_exon_variant	0.7	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472660	n.815T>C	non_coding_transcript_exon_variant	0.69	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472692	n.847T>C	non_coding_transcript_exon_variant	0.57	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472714	n.869A>G	non_coding_transcript_exon_variant	0.59	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472755	n.910G>A	non_coding_transcript_exon_variant	0.32	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1476164	n.2507A>G	non_coding_transcript_exon_variant	0.25	capreomycin	Uncertain significance
rrl	1476164	n.2507A>G	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476194	n.2537A>G	non_coding_transcript_exon_variant	0.22	capreomycin	Not assoc w R
rrl	1476194	n.2537A>G	non_coding_transcript_exon_variant	0.22	linezolid	Uncertain significance
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.21	capreomycin	Not assoc w R
rrl	1476200	n.2543A>T	non_coding_transcript_exon_variant	0.21	linezolid	Uncertain significance
rrl	1476201	n.2544C>T	non_coding_transcript_exon_variant	0.2	capreomycin	Not assoc w R
rrl	1476201	n.2544C>T	non_coding_transcript_exon_variant	0.2	linezolid	Uncertain significance
rrl	1476214	n.2557G>T	non_coding_transcript_exon_variant	0.35	capreomycin	Uncertain significance
rrl	1476214	n.2557G>T	non_coding_transcript_exon_variant	0.35	linezolid	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.36	capreomycin	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.36	linezolid	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.35	capreomycin	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.35	linezolid	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476252	n.2595T>G	non_coding_transcript_exon_variant	0.34	capreomycin	Uncertain significance
rrl	1476252	n.2595T>G	non_coding_transcript_exon_variant	0.34	linezolid	Uncertain significance
rrl	1476253	n.2596A>G	non_coding_transcript_exon_variant	0.33	capreomycin
rrl	1476253	n.2596A>G	non_coding_transcript_exon_variant	0.33	linezolid
rrl	1476256	n.2599A>G	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476256	n.2599A>G	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.33	capreomycin	Not assoc w R
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.3	capreomycin	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.3	linezolid	Uncertain significance
rrl	1476294	n.2637A>G	non_coding_transcript_exon_variant	0.25	capreomycin	Uncertain significance
rrl	1476294	n.2637A>G	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476295	n.2638C>G	non_coding_transcript_exon_variant	0.25	capreomycin	Uncertain significance
rrl	1476295	n.2638C>G	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476296	n.2639C>T	non_coding_transcript_exon_variant	0.24	capreomycin	Uncertain significance
rrl	1476296	n.2639C>T	non_coding_transcript_exon_variant	0.24	linezolid	Uncertain significance
rrl	1476297	n.2640C>A	non_coding_transcript_exon_variant	0.24	capreomycin	Uncertain significance
rrl	1476297	n.2640C>A	non_coding_transcript_exon_variant	0.24	linezolid	Uncertain significance
rrl	1476299	n.2642C>G	non_coding_transcript_exon_variant	0.24	capreomycin
rrl	1476299	n.2642C>G	non_coding_transcript_exon_variant	0.24	linezolid
rrl	1476300	n.2643G>T	non_coding_transcript_exon_variant	0.23	capreomycin
rrl	1476300	n.2643G>T	non_coding_transcript_exon_variant	0.23	linezolid
rrl	1476301	n.2644A>T	non_coding_transcript_exon_variant	0.24	capreomycin	Uncertain significance
rrl	1476301	n.2644A>T	non_coding_transcript_exon_variant	0.24	linezolid	Uncertain significance
rrl	1476308	n.2651G>C	non_coding_transcript_exon_variant	0.23	capreomycin
rrl	1476308	n.2651G>C	non_coding_transcript_exon_variant	0.23	linezolid
rrl	1476311	n.2654G>C	non_coding_transcript_exon_variant	0.25	capreomycin	Uncertain significance
rrl	1476311	n.2654G>C	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476312	n.2655T>C	non_coding_transcript_exon_variant	0.26	capreomycin	Uncertain significance
rrl	1476312	n.2655T>C	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1476337	n.2680C>T	non_coding_transcript_exon_variant	0.25	capreomycin	Uncertain significance
rrl	1476337	n.2680C>T	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
pncA	2289047	c.195C>T	synonymous_variant	0.96	pyrazinamide	Not assoc w R
gid	4407588	c.615A>G	synonymous_variant	0.98	streptomycin	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