TB-Profiler

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.8	Euro-American (mainly T)	RD219	1.0

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rrs	1472733	n.888G>A	non_coding_transcript_exon_variant	0.13	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	7362	p.Glu21Gln	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
Rv0565c	656265	c.1204_1205delAC	frameshift_variant	1.0	ethionamide	Uncertain significance
nusG	734658	c.405A>G	synonymous_variant	1.0	rifampicin	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472616	n.771G>A	non_coding_transcript_exon_variant	0.12	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472655	n.810G>A	non_coding_transcript_exon_variant	0.2	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472658	n.813G>A	non_coding_transcript_exon_variant	0.18	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472661	n.816A>G	non_coding_transcript_exon_variant	0.18	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472670	n.825G>T	non_coding_transcript_exon_variant	0.14	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472673	n.828T>G	non_coding_transcript_exon_variant	0.17	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472675	n.830T>C	non_coding_transcript_exon_variant	0.17	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472677	n.832C>T	non_coding_transcript_exon_variant	0.16	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472681	n.837_838delTT	non_coding_transcript_exon_variant	0.15	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472690	n.845C>A	non_coding_transcript_exon_variant	0.18	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472697	n.852T>C	non_coding_transcript_exon_variant	0.13	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472713	n.868T>C	non_coding_transcript_exon_variant	0.14	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472716	n.871C>T	non_coding_transcript_exon_variant	0.14	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472742	n.897C>T	non_coding_transcript_exon_variant	0.13	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472744	n.899A>G	non_coding_transcript_exon_variant	0.13	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473035	n.1190G>A	non_coding_transcript_exon_variant	0.17	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473055	n.1210C>T	non_coding_transcript_exon_variant	0.14	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473056	n.1211A>T	non_coding_transcript_exon_variant	0.14	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473145	n.1300C>T	non_coding_transcript_exon_variant	0.11	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473166	n.1321G>A	non_coding_transcript_exon_variant	0.12	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	linezolid	Not assoc w R
rrl	1474777	n.1120T>C	non_coding_transcript_exon_variant	0.11	capreomycin	Not assoc w R
rrl	1474777	n.1120T>C	non_coding_transcript_exon_variant	0.11	linezolid	Uncertain significance
rrl	1474779	n.1122G>A	non_coding_transcript_exon_variant	0.13	capreomycin	Uncertain significance
rrl	1474779	n.1122G>A	non_coding_transcript_exon_variant	0.13	linezolid	Uncertain significance
rrl	1474782	n.1125G>A	non_coding_transcript_exon_variant	0.12	capreomycin	Not assoc w R
rrl	1474782	n.1125G>A	non_coding_transcript_exon_variant	0.12	linezolid	Uncertain significance
rrl	1474794	n.1137C>T	non_coding_transcript_exon_variant	0.18	capreomycin	Uncertain significance
rrl	1474794	n.1137C>T	non_coding_transcript_exon_variant	0.18	linezolid	Uncertain significance
rrl	1474823	n.1166C>G	non_coding_transcript_exon_variant	0.15	capreomycin	Uncertain significance
rrl	1474823	n.1166C>G	non_coding_transcript_exon_variant	0.15	linezolid	Uncertain significance
rrl	1474831	n.1174A>T	non_coding_transcript_exon_variant	0.14	capreomycin	Uncertain significance
rrl	1474831	n.1174A>T	non_coding_transcript_exon_variant	0.14	linezolid	Uncertain significance
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.19	capreomycin	Uncertain significance
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.19	linezolid
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.18	capreomycin	Uncertain significance
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.18	linezolid
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.25	capreomycin	Not assoc w R
rrl	1476260	n.2603A>G	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476311	n.2654G>C	non_coding_transcript_exon_variant	0.18	capreomycin	Uncertain significance
rrl	1476311	n.2654G>C	non_coding_transcript_exon_variant	0.18	linezolid	Uncertain significance
rrl	1476312	n.2655T>C	non_coding_transcript_exon_variant	0.18	capreomycin	Uncertain significance
rrl	1476312	n.2655T>C	non_coding_transcript_exon_variant	0.18	linezolid	Uncertain significance
rrl	1476353	n.2696G>T	non_coding_transcript_exon_variant	0.19	capreomycin	Uncertain significance
rrl	1476353	n.2696G>T	non_coding_transcript_exon_variant	0.19	linezolid	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.17	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.17	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.15	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.15	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.2	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.2	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.16	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.16	linezolid	Uncertain significance
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.17	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.17	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.2	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.2	linezolid	Uncertain significance
PPE35	2168149	p.Pro822Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
PPE35	2170048	p.Leu189Val	missense_variant	0.62	pyrazinamide
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
Rv3236c	3613636	c.-520A>G	upstream_gene_variant	1.0	pyrazinamide	Not assoc w R
clpC1	4039729	p.Asp326Asn	missense_variant	0.86	pyrazinamide	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R

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