TB-Profiler

TB-Profiler result

Run: 9be87ecd-8004-4ba3-9452-955718d62a07

This result has been migrated from an older version of TB-Profiler. Some information may be missing, and it has not been profiled using the latest mutation database. It is advised to re-run the analysis.

Summary

Run ID: 9be87ecd-8004-4ba3-9452-955718d62a07

Sample name:

Date: 22-11-2023 10:23:41

Number of reads: 747727

Percentage reads mapped: 96.28

Median coverage: 30

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	1.0

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin	rpoB	p.Ser450Leu	Assoc w R
isoniazid	inhA	p.Ile21Val	Uncertain significance
isoniazid	katG	c.2028dupG	Uncertain significance
c.2020dupG	katG	Uncertain significance
c.1814delC	Uncertain significance
c.1735delA	Uncertain significance
c.1719delT	Uncertain significance
c.1359delC	Uncertain significance
c.1231_1232delGC	Uncertain significance
c.1073delG	Uncertain significance
p.Ser315Thr	Assoc w R
c.756dupT	Uncertain significance
c.702delG	Uncertain significance
c.596dupG	Uncertain significance
c.500dupT	Uncertain significance
c.371dupG	Uncertain significance
c.332delG	Uncertain significance
c.235dupG	Uncertain significance
c.219delT	Uncertain significance
c.17delC	Assoc w R - interim
c.17delC	Uncertain significance
ethambutol	embB	p.Met306Val	Assoc w R
pyrazinamide	pncA	c.106delG	Uncertain significance
pyrazinamide	pncA	p.Leu27Pro	Assoc w R
moxifloxacin	gyrA	p.Ala90Val	Assoc w R
levofloxacin	gyrA	p.Ala90Val	Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin	rpsL	p.Lys43Arg	Assoc w R
streptomycin	gid	c.351delG	Assoc w R - interim
amikacin	rrs	n.1401A>G	Assoc w R
kanamycin	rrs	n.1401A>G	Assoc w R
capreomycin	rrs	n.1401A>G	Assoc w R
capreomycin	tlyA	c.125delC	Uncertain significance
c.159delC	tlyA	Uncertain significance
c.207delA	Uncertain significance
c.273_274insG	Uncertain significance
c.413_414delGC	Uncertain significance
c.424delG	Uncertain significance
clofazimine
ethionamide	ethA	c.1451delC	Uncertain significance
ethionamide	ethA	c.1054dupG	Uncertain significance
c.659delG	Uncertain significance
c.597delC	Assoc w R - interim
c.597delC	Uncertain significance
c.437delG	Uncertain significance
c.233delG	Uncertain significance
c.228delC	Uncertain significance
c.21delT	Uncertain significance
c.16delG	Uncertain significance
para-aminosalicylic_acid
cycloserine

Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence
gyrA	7570	p.Ala90Val	missense_variant	1.0	ofloxacin	Uncertain significance
					moxifloxacin	Assoc w R
					levofloxacin	Assoc w R
					fluoroquinolones	Uncertain significance
					ciprofloxacin	Uncertain significance
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
rpsL	781687	p.Lys43Arg	missense_variant	0.97	streptomycin	Assoc w R
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	1.0	kanamycin	Assoc w R
					capreomycin	Assoc w R
					aminoglycosides	Uncertain significance
					amikacin	Assoc w R
inhA	1674262	p.Ile21Val	missense_variant	1.0	isoniazid	Uncertain significance
tlyA	1918063	c.125delC	frameshift_variant	0.12	capreomycin	Uncertain significance
tlyA	1918096	c.159delC	frameshift_variant	0.4	capreomycin	Uncertain significance
tlyA	1918143	c.207delA	frameshift_variant	0.12	capreomycin	Uncertain significance
tlyA	1918212	c.273_274insG	frameshift_variant	0.14	capreomycin	Uncertain significance
tlyA	1918351	c.413_414delGC	frameshift_variant	0.37	capreomycin	Uncertain significance
tlyA	1918361	c.424delG	frameshift_variant	0.13	capreomycin	Uncertain significance
katG	2154083	c.2028dupG	frameshift_variant	0.21	isoniazid	Uncertain significance
katG	2154091	c.2020dupG	frameshift_variant	0.13	isoniazid	Uncertain significance
katG	2154297	c.1814delC	frameshift_variant	0.17	isoniazid	Uncertain significance
katG	2154376	c.1735delA	frameshift_variant	0.12	isoniazid	Uncertain significance
katG	2154392	c.1719delT	frameshift_variant	0.19	isoniazid	Uncertain significance
katG	2154752	c.1359delC	frameshift_variant	0.38	isoniazid	Uncertain significance
katG	2154879	c.1231_1232delGC	frameshift_variant	0.2	isoniazid	Uncertain significance
katG	2155038	c.1073delG	frameshift_variant	0.18	isoniazid	Uncertain significance
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R
katG	2155355	c.756dupT	frameshift_variant	0.13	isoniazid	Uncertain significance
katG	2155409	c.702delG	frameshift_variant	0.11	isoniazid	Uncertain significance
katG	2155515	c.596dupG	frameshift_variant	0.12	isoniazid	Uncertain significance
katG	2155611	c.500dupT	frameshift_variant	0.26	isoniazid	Uncertain significance
katG	2155740	c.371dupG	frameshift_variant	0.12	isoniazid	Uncertain significance
katG	2155779	c.332delG	frameshift_variant	0.27	isoniazid	Uncertain significance
katG	2155876	c.235dupG	frameshift_variant	0.11	isoniazid	Uncertain significance
katG	2155892	c.219delT	frameshift_variant	0.11	isoniazid	Uncertain significance
katG	2156094	c.17delC	frameshift_variant	0.14	isoniazid	Assoc w R - interim
katG	2156094	c.17delC	frameshift_variant	0.14	isoniazid	Uncertain significance
pncA	2289135	c.106delG	frameshift_variant	0.15	pyrazinamide	Uncertain significance
pncA	2289162	p.Leu27Pro	missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247429	p.Met306Val	missense_variant	1.0	ethambutol	Assoc w R
ethA	4326022	c.1451delC	frameshift_variant	0.12	ethionamide	Uncertain significance
ethA	4326419	c.1054dupG	frameshift_variant	0.13	ethionamide	Uncertain significance
ethA	4326814	c.659delG	frameshift_variant	0.28	ethionamide	Uncertain significance
ethA	4326876	c.597delC	frameshift_variant	0.14	ethionamide	Assoc w R - interim
ethA	4326876	c.597delC	frameshift_variant	0.14	ethionamide	Uncertain significance
ethA	4327036	c.437delG	frameshift_variant	0.33	ethionamide	Uncertain significance
ethA	4327240	c.233delG	frameshift_variant	0.24	ethionamide	Uncertain significance
ethA	4327245	c.228delC	frameshift_variant	0.18	ethionamide	Uncertain significance
ethA	4327452	c.21delT	frameshift_variant	0.15	ethionamide	Uncertain significance
ethA	4327457	c.16delG	frameshift_variant	0.4	ethionamide	Uncertain significance
gid	4407851	c.351delG	frameshift_variant	0.15	streptomycin	Assoc w R - interim

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
gyrB	5251	c.17delA	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	5302	c.66delG	frameshift_variant	0.2	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	5320	c.84dupA	frameshift_variant	0.17	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	5552	c.315delC	frameshift_variant	0.13	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	5608	c.371delG	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	5623	c.386delA	frameshift_variant	0.13	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	5701	c.466delC	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	6244	c.1007dupA	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	6275	c.1038delC	frameshift_variant	0.14	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	6385	c.1149delT	frameshift_variant	0.15	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	6639	c.1405delA	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrB	6799	c.1562delA	frameshift_variant	0.29	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	7340	c.40_41delCG	frameshift_variant	0.14	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	7362	p.Glu21Gln	missense_variant	1.0	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	7459	c.160delC	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	7533	c.234delC	frameshift_variant	0.2	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	7585	p.Ser95Thr	missense_variant	1.0	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	7929	c.630delC	frameshift_variant	0.33	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	7970	c.672dupA	frameshift_variant	0.19	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	8046	c.747delC	frameshift_variant	0.2	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	8131	c.832delG	frameshift_variant	0.14	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	8659	c.1359delC	frameshift_variant	0.16	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	8688	c.1389delC	frameshift_variant	0.23	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	8710	c.1413delA	frameshift_variant	0.15	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	8935	c.1637delG	frameshift_variant	0.12	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	9188	c.1890delG	frameshift_variant	0.15	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	9304	p.Gly668Asp	missense_variant	1.0	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	9423	c.2123delA	frameshift_variant	0.18	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	9426	c.2126delA	frameshift_variant	0.14	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
gyrA	9687	c.2388delG	frameshift_variant	0.35	fluoroquinolones
					moxifloxacin
					levofloxacin
					ciprofloxacin
					ofloxacin
fgd1	490621	c.-161delG	upstream_gene_variant	0.12	delamanid
fgd1	490683	c.-100_-99insG	upstream_gene_variant	0.11	delamanid
fgd1	490736	c.-46delC	upstream_gene_variant	0.4	delamanid
fgd1	490901	c.123delT	frameshift_variant	0.13	delamanid
fgd1	491008	c.231delC	frameshift_variant	0.14	delamanid
fgd1	491083	c.305dupT	frameshift_variant	0.14	delamanid
fgd1	491229	c.450dupT	frameshift_variant&stop_gained	0.12	delamanid
fgd1	491288	c.506dupG	frameshift_variant	0.15	delamanid
fgd1	491570	c.789delC	frameshift_variant	0.12	delamanid
fgd1	491742	c.960T>C	synonymous_variant	1.0	delamanid
mshA	575210	c.-137delG	upstream_gene_variant	0.12	ethionamide
mshA	575210	c.-137delG	upstream_gene_variant	0.12	isoniazid
mshA	575655	c.310delG	frameshift_variant	0.12	ethionamide
mshA	575655	c.310delG	frameshift_variant	0.12	isoniazid
mshA	575722	c.378delC	frameshift_variant	0.31	ethionamide
mshA	575722	c.378delC	frameshift_variant	0.31	isoniazid
mshA	575830	c.485delG	frameshift_variant	0.45	ethionamide
mshA	575830	c.485delG	frameshift_variant	0.45	isoniazid
mshA	575859	c.513dupG	frameshift_variant	0.17	ethionamide
mshA	575859	c.513dupG	frameshift_variant	0.17	isoniazid
mshA	576020	c.676dupT	frameshift_variant	0.19	ethionamide
mshA	576020	c.676dupT	frameshift_variant	0.19	isoniazid
mshA	576264	c.919delG	frameshift_variant	0.23	ethionamide
mshA	576264	c.919delG	frameshift_variant	0.23	isoniazid
mshA	576325	c.981dupT	frameshift_variant	0.25	ethionamide
mshA	576325	c.981dupT	frameshift_variant	0.25	isoniazid
mshA	576477	c.1131dupG	frameshift_variant	0.15	ethionamide
mshA	576477	c.1131dupG	frameshift_variant	0.15	isoniazid
mshA	576483	c.1137dupC	frameshift_variant	0.12	ethionamide
mshA	576483	c.1137dupC	frameshift_variant	0.12	isoniazid
mshA	576584	c.1241delG	frameshift_variant	0.13	ethionamide
mshA	576584	c.1241delG	frameshift_variant	0.13	isoniazid
ccsA	619743	c.-147dupA	upstream_gene_variant	0.14	capreomycin
ccsA	619743	c.-147dupA	upstream_gene_variant	0.14	amikacin
ccsA	619830	c.-60delT	upstream_gene_variant	0.34	capreomycin
ccsA	619830	c.-60delT	upstream_gene_variant	0.34	amikacin
ccsA	619951	c.61delG	frameshift_variant	0.12	capreomycin
ccsA	619951	c.61delG	frameshift_variant	0.12	amikacin
ccsA	620048	c.160delG	frameshift_variant	0.24	capreomycin
ccsA	620048	c.160delG	frameshift_variant	0.24	amikacin
ccsA	620205	c.317delC	frameshift_variant	0.13	capreomycin
ccsA	620205	c.317delC	frameshift_variant	0.13	amikacin
ccsA	620546	c.660delC	frameshift_variant	0.12	capreomycin
ccsA	620546	c.660delC	frameshift_variant	0.12	amikacin
ccsA	620625	p.Ile245Met	missense_variant	1.0	capreomycin	Uncertain significance
ccsA	620625	p.Ile245Met	missense_variant	1.0	amikacin	Uncertain significance
ccsA	620846	c.957dupG	frameshift_variant	0.11	capreomycin
ccsA	620846	c.957dupG	frameshift_variant	0.11	amikacin
rpoB	759726	c.-80delA	upstream_gene_variant	0.14	rifampicin
rpoB	759783	c.-24C>T	upstream_gene_variant	0.11	rifampicin
rpoB	759808	c.4delG	frameshift_variant	0.23	rifampicin
rpoB	759910	c.105delC	frameshift_variant	0.12	rifampicin
rpoB	760017	c.215dupG	frameshift_variant	0.11	rifampicin
rpoB	760334	c.531dupC	frameshift_variant	0.11	rifampicin
rpoB	760431	c.626delA	frameshift_variant	0.29	rifampicin
rpoB	760472	c.669delA	frameshift_variant	0.13	rifampicin
rpoB	760479	c.675delG	frameshift_variant	0.14	rifampicin
rpoB	760643	c.842delC	frameshift_variant	0.12	rifampicin
rpoB	760797	c.992delA	frameshift_variant	0.14	rifampicin
rpoB	761107	c.1303delG	frameshift_variant	0.28	rifampicin
rpoB	761351	c.1547delG	frameshift_variant	0.13	rifampicin
rpoB	761559	c.1755delC	frameshift_variant	0.24	rifampicin
rpoB	761895	c.2091delC	frameshift_variant	0.15	rifampicin
rpoB	761918	c.2114delG	frameshift_variant	0.19	rifampicin
rpoB	761960	c.2156delC	frameshift_variant	0.12	rifampicin
rpoB	762121	c.2316delC	frameshift_variant	0.16	rifampicin
rpoB	762147	c.2345dupG	frameshift_variant	0.18	rifampicin
rpoB	762371	c.2567delC	frameshift_variant	0.32	rifampicin
rpoB	762510	c.2706delC	frameshift_variant	0.12	rifampicin
rpoB	762515	c.2711delG	frameshift_variant	0.25	rifampicin
rpoB	762579	c.2777dupT	frameshift_variant	0.14	rifampicin
rpoB	762637	c.2836delG	frameshift_variant	0.12	rifampicin
rpoB	762662	c.2857delC	frameshift_variant	0.17	rifampicin
rpoC	763031	c.-339T>C	upstream_gene_variant	1.0	rifampicin
rpoB	763257	c.3454delG	frameshift_variant	0.13	rifampicin
rpoC	763453	c.89dupA	frameshift_variant	0.12	rifampicin
rpoC	763883	c.527delA	frameshift_variant	0.12	rifampicin
rpoC	764167	c.800dupA	frameshift_variant	0.12	rifampicin
rpoC	764534	c.1167delG	frameshift_variant	0.15	rifampicin
rpoC	764808	c.1444dupC	frameshift_variant	0.13	rifampicin
rpoC	765147	c.1779_1780delCG	frameshift_variant	0.21	rifampicin
rpoC	765348	p.Asp660Gly	missense_variant	0.12	rifampicin
rpoC	765569	c.2202delC	frameshift_variant	0.12	rifampicin
rpoC	765724	c.2357delG	frameshift_variant	0.12	rifampicin
rpoC	765747	c.2382dupC	frameshift_variant	0.19	rifampicin
rpoC	765754	c.2386dupG	frameshift_variant	0.12	rifampicin
rpoC	765996	c.2628delT	frameshift_variant	0.16	rifampicin
rpoC	766349	c.2982delC	frameshift_variant	0.26	rifampicin
rpoC	766423	c.3056delG	frameshift_variant	0.17	rifampicin
rpoC	766508	c.3141delC	frameshift_variant	0.27	rifampicin
rpoC	766514	c.3146delT	frameshift_variant	0.24	rifampicin
rpoC	766593	c.3226delG	frameshift_variant	0.22	rifampicin
rpoC	766914	c.3547delC	frameshift_variant	0.2	rifampicin
rpoC	766975	c.3606delC	frameshift_variant	0.14	rifampicin
rpoC	767004	c.3637delG	frameshift_variant	0.11	rifampicin
rpoC	767117	c.3752dupA	frameshift_variant	0.12	rifampicin
rpoC	767149	c.3782delG	frameshift_variant	0.55	rifampicin
rpoC	767279	c.3912delC	frameshift_variant	0.17	rifampicin
mmpL5	775614	c.2866delG	frameshift_variant	0.12	clofazimine
mmpL5	775614	c.2866delG	frameshift_variant	0.12	bedaquiline
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	776288	c.2192delG	frameshift_variant	0.28	clofazimine
mmpL5	776288	c.2192delG	frameshift_variant	0.28	bedaquiline
mmpL5	776311	c.2169delA	frameshift_variant	0.16	clofazimine
mmpL5	776311	c.2169delA	frameshift_variant	0.16	bedaquiline
mmpL5	776329	c.2151delG	frameshift_variant	0.12	clofazimine
mmpL5	776329	c.2151delG	frameshift_variant	0.12	bedaquiline
mmpL5	776673	c.1807delG	frameshift_variant	0.15	clofazimine
mmpL5	776673	c.1807delG	frameshift_variant	0.15	bedaquiline
mmpL5	776823	c.1657delA	frameshift_variant	0.13	clofazimine
mmpL5	776823	c.1657delA	frameshift_variant	0.13	bedaquiline
mmpL5	777024	c.1456delC	frameshift_variant	0.46	clofazimine
mmpL5	777024	c.1456delC	frameshift_variant	0.46	bedaquiline
mmpL5	777092	c.1388dupT	frameshift_variant	0.2	clofazimine
mmpL5	777092	c.1388dupT	frameshift_variant	0.2	bedaquiline
mmpL5	777167	c.1313delT	frameshift_variant	0.21	clofazimine
mmpL5	777167	c.1313delT	frameshift_variant	0.21	bedaquiline
mmpL5	777233	c.1247delA	frameshift_variant	0.31	clofazimine
mmpL5	777233	c.1247delA	frameshift_variant	0.31	bedaquiline
mmpL5	777269	c.1211delG	frameshift_variant	0.15	clofazimine
mmpL5	777269	c.1211delG	frameshift_variant	0.15	bedaquiline
mmpL5	777403	c.1077delC	frameshift_variant	0.25	clofazimine
mmpL5	777403	c.1077delC	frameshift_variant	0.25	bedaquiline
mmpL5	777794	c.684delG	frameshift_variant	0.19	clofazimine
mmpL5	777794	c.684delG	frameshift_variant	0.19	bedaquiline
mmpL5	778086	c.394delG	frameshift_variant	0.18	clofazimine
mmpL5	778086	c.394delG	frameshift_variant	0.18	bedaquiline
mmpL5	778116	c.364delC	frameshift_variant	0.35	clofazimine
mmpL5	778116	c.364delC	frameshift_variant	0.35	bedaquiline
mmpL5	778190	c.290delG	frameshift_variant	0.15	clofazimine
mmpL5	778190	c.290delG	frameshift_variant	0.15	bedaquiline
mmpS5	778602	c.303delC	frameshift_variant	0.12	clofazimine
mmpS5	778602	c.303delC	frameshift_variant	0.12	bedaquiline
mmpS5	778617	c.289delC	frameshift_variant	0.13	clofazimine
mmpS5	778617	c.289delC	frameshift_variant	0.13	bedaquiline
mmpS5	778649	c.256delC	frameshift_variant	0.33	clofazimine
mmpS5	778649	c.256delC	frameshift_variant	0.33	bedaquiline
mmpR5	779181	c.198delG	frameshift_variant	0.16	clofazimine	Uncertain significance
mmpR5	779181	c.198delG	frameshift_variant	0.16	bedaquiline	Uncertain significance
mmpR5	779217	c.231delT	frameshift_variant	0.15	clofazimine
mmpR5	779217	c.231delT	frameshift_variant	0.15	bedaquiline
mmpR5	779446	c.460delC	frameshift_variant	0.16	clofazimine
mmpR5	779446	c.460delC	frameshift_variant	0.16	bedaquiline
mmpS5	779597	c.-693delA	upstream_gene_variant	0.33	clofazimine
mmpS5	779597	c.-693delA	upstream_gene_variant	0.33	bedaquiline
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
mmpS5	779657	c.-753delT	upstream_gene_variant	0.14	clofazimine
mmpS5	779657	c.-753delT	upstream_gene_variant	0.14	bedaquiline
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Uncertain significance
rpsL	781520	c.-39delA	upstream_gene_variant	0.14	streptomycin
rpsL	781902	c.344delG	frameshift_variant	0.35	streptomycin
rpsL	781927	c.371delG	frameshift_variant	0.16	streptomycin
rplC	800810	c.4delG	frameshift_variant	0.26	linezolid
rplC	800863	c.58delA	frameshift_variant	0.12	linezolid
rplC	800981	c.176delC	frameshift_variant	0.21	linezolid
rplC	801031	c.224delT	frameshift_variant	0.2	linezolid
rplC	801229	c.420_421insC	frameshift_variant	0.13	linezolid
rplC	801245	c.439delC	frameshift_variant	0.16	linezolid
rplC	801288	c.482delT	frameshift_variant	0.11	linezolid
rplC	801309	c.504delG	frameshift_variant	0.14	linezolid
fbiC	1302823	c.-107delC	upstream_gene_variant	0.17	delamanid
fbiC	1303147	c.219delC	frameshift_variant	0.29	delamanid
fbiC	1303200	c.273dupT	frameshift_variant	0.13	delamanid
fbiC	1303393	c.465delG	frameshift_variant	0.21	delamanid
fbiC	1303444	c.516delC	frameshift_variant	0.26	delamanid
fbiC	1303635	c.708delA	frameshift_variant	0.17	delamanid
fbiC	1304010	c.1081delA	frameshift_variant	0.12	delamanid
fbiC	1304150	c.1223delC	frameshift_variant	0.19	delamanid
fbiC	1304161	c.1235dupG	frameshift_variant	0.18	delamanid
fbiC	1304628	c.1700delT	frameshift_variant	0.18	delamanid
fbiC	1304707	c.1778delT	frameshift_variant	0.12	delamanid
fbiC	1304766	c.1838delG	frameshift_variant	0.26	delamanid
fbiC	1304794	c.1867delG	frameshift_variant	0.12	delamanid
fbiC	1304830	c.1904dupC	frameshift_variant	0.17	delamanid
fbiC	1304991	c.2062delT	frameshift_variant	0.24	delamanid
Rv1258c	1406105	c.1235_1236insC	frameshift_variant	0.12	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406200	c.1140dupT	frameshift_variant	0.16	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406298	c.1042dupG	frameshift_variant	0.12	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406322	c.1018delG	frameshift_variant	0.12	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406373	c.967delC	frameshift_variant	0.28	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406441	c.899delT	frameshift_variant	0.13	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406536	c.804delC	frameshift_variant	0.24	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406549	c.791delT	frameshift_variant	0.18	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406658	c.682delC	frameshift_variant	0.12	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406719	c.621delG	frameshift_variant	0.15	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406760	c.580_581insC	frameshift_variant	1.0	streptomycin	Uncertain significance
					pyrazinamide	Uncertain significance
					isoniazid	Uncertain significance
Rv1258c	1406802	c.538delG	frameshift_variant	0.43	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1406898	c.442delG	frameshift_variant	0.21	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1407050	c.290dupG	frameshift_variant	0.2	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1407081	c.259delG	frameshift_variant	0.14	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1407127	c.213delT	frameshift_variant	0.12	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1407388	c.-48delT	upstream_gene_variant	0.12	streptomycin
					pyrazinamide
					isoniazid
Rv1258c	1407444	c.-105delG	upstream_gene_variant	0.3	streptomycin
					pyrazinamide
					isoniazid
embR	1416196	c.1151delC	frameshift_variant	0.12	ethambutol
embR	1416322	c.1025delA	frameshift_variant	0.12	ethambutol
embR	1416439	c.908_909insC	frameshift_variant	0.12	ethambutol
embR	1416500	c.847delG	frameshift_variant	0.23	ethambutol
embR	1416666	c.681delC	frameshift_variant	0.16	ethambutol
embR	1416861	c.486dupT	frameshift_variant	0.14	ethambutol
embR	1416989	c.358delA	frameshift_variant	0.42	ethambutol	Uncertain significance
embR	1417029	c.318dupC	frameshift_variant	0.17	ethambutol
embR	1417105	c.242delA	frameshift_variant	0.12	ethambutol
embR	1417184	c.163delC	frameshift_variant	0.12	ethambutol
atpE	1460931	c.-113delT	upstream_gene_variant	0.29	bedaquiline
atpE	1461197	c.155delC	frameshift_variant	0.12	bedaquiline
rrs	1471659	n.-187C>T	upstream_gene_variant	0.98	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471721	n.-125_-124insT	upstream_gene_variant	0.12	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471733	n.-105dupT	upstream_gene_variant	0.17	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471771	n.-75_-74insG	upstream_gene_variant	0.14	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471782	n.-57delT	upstream_gene_variant	0.2	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471836	n.-9delG	upstream_gene_variant	0.12	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471845	n.4delT	non_coding_transcript_exon_variant	0.12	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1471975	n.133delC	non_coding_transcript_exon_variant	0.35	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472118	n.275delG	non_coding_transcript_exon_variant	0.12	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472263	n.420delT	non_coding_transcript_exon_variant	0.43	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472284	n.439C>T	non_coding_transcript_exon_variant	0.12	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472287	n.442C>A	non_coding_transcript_exon_variant	0.11	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472288	n.443A>C	non_coding_transcript_exon_variant	0.11	linezolid
					kanamycin
					capreomycin
					amikacin	Uncertain significance
					aminoglycosides
					streptomycin
rrs	1472386	n.543delT	non_coding_transcript_exon_variant	0.13	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472672	n.830delT	non_coding_transcript_exon_variant	0.12	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1472997	n.1154delC	non_coding_transcript_exon_variant	0.14	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrs	1473036	n.1192delC	non_coding_transcript_exon_variant	0.3	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
rrl	1473395	n.-263_-262insA	upstream_gene_variant	0.16	linezolid
rrl	1473645	n.-12delT	upstream_gene_variant	0.22	linezolid
rrl	1473839	n.184delA	non_coding_transcript_exon_variant	0.14	linezolid
rrl	1473862	n.205_206insG	non_coding_transcript_exon_variant	0.12	linezolid
rrl	1474001	n.346delG	non_coding_transcript_exon_variant	0.14	linezolid
rrl	1474084	n.431delA	non_coding_transcript_exon_variant	0.14	linezolid
rrl	1474694	n.1040delA	non_coding_transcript_exon_variant	0.12	linezolid
rrl	1474706	n.1051delC	non_coding_transcript_exon_variant	0.18	linezolid
rrl	1475205	n.1551delC	non_coding_transcript_exon_variant	0.39	linezolid
rrl	1475260	n.1608dupG	non_coding_transcript_exon_variant	0.12	linezolid
rrl	1475571	n.1921delC	non_coding_transcript_exon_variant	0.17	linezolid
rrl	1475678	n.2021delA	non_coding_transcript_exon_variant	0.14	linezolid
rrl	1475951	n.2298dupA	non_coding_transcript_exon_variant	0.21	linezolid
rrl	1475966	n.2310_2311delCT	non_coding_transcript_exon_variant	0.12	linezolid
rrl	1476112	n.2458delT	non_coding_transcript_exon_variant	0.18	linezolid
rrl	1476229	n.2574delA	non_coding_transcript_exon_variant	0.12	linezolid
rrl	1476378	n.2724delG	non_coding_transcript_exon_variant	0.32	linezolid
rrl	1476522	n.2866delT	non_coding_transcript_exon_variant	0.12	linezolid
fabG1	1673158	c.-281dupT	upstream_gene_variant	0.15	ethionamide
fabG1	1673158	c.-281dupT	upstream_gene_variant	0.15	isoniazid
fabG1	1673209	c.-230dupT	upstream_gene_variant	0.21	ethionamide
fabG1	1673209	c.-230dupT	upstream_gene_variant	0.21	isoniazid
fabG1	1673411	c.-28delG	upstream_gene_variant	0.15	ethionamide
fabG1	1673411	c.-28delG	upstream_gene_variant	0.15	isoniazid
fabG1	1673429	c.-10delG	upstream_gene_variant	0.12	ethionamide
fabG1	1673429	c.-10delG	upstream_gene_variant	0.12	isoniazid
fabG1	1673510	c.78dupG	frameshift_variant	0.14	ethionamide
fabG1	1673510	c.78dupG	frameshift_variant	0.14	isoniazid
fabG1	1673700	c.263delA	frameshift_variant	0.17	ethionamide
fabG1	1673700	c.263delA	frameshift_variant	0.17	isoniazid
fabG1	1674074	c.635delG	frameshift_variant	0.15	ethionamide
fabG1	1674074	c.635delG	frameshift_variant	0.15	isoniazid
inhA	1674352	c.153delC	frameshift_variant	0.12	ethionamide
inhA	1674352	c.153delC	frameshift_variant	0.12	isoniazid
inhA	1674413	c.214delG	frameshift_variant	0.16	ethionamide
inhA	1674413	c.214delG	frameshift_variant	0.16	isoniazid
inhA	1674468	c.271delG	frameshift_variant	0.33	ethionamide
inhA	1674468	c.271delG	frameshift_variant	0.33	isoniazid
inhA	1674916	c.717delC	frameshift_variant	0.13	ethionamide
inhA	1674916	c.717delC	frameshift_variant	0.13	isoniazid
inhA	1674923	c.724delG	frameshift_variant	0.13	ethionamide
inhA	1674923	c.724delG	frameshift_variant	0.13	isoniazid
rpsA	1833414	c.-128_-127insT	upstream_gene_variant	0.15	pyrazinamide
rpsA	1833504	c.-37delC	upstream_gene_variant	0.21	pyrazinamide
rpsA	1833512	c.-29delC	upstream_gene_variant	0.26	pyrazinamide
rpsA	1833622	c.85delA	frameshift_variant	0.2	pyrazinamide
rpsA	1833803	c.265delC	frameshift_variant	0.28	pyrazinamide
rpsA	1834175	c.636A>C	synonymous_variant	1.0	pyrazinamide
rpsA	1834722	c.1184delG	frameshift_variant	0.32	pyrazinamide
rpsA	1834763	c.1226dupA	frameshift_variant	0.27	pyrazinamide
rpsA	1834885	c.1345delT	frameshift_variant	0.23	pyrazinamide
rpsA	1834890	c.1351delG	frameshift_variant	0.17	pyrazinamide
rpsA	1834910	c.1373dupA	frameshift_variant	0.12	pyrazinamide
rpsA	1834955	c.1417delC	frameshift_variant	0.22	pyrazinamide
rpsA	1834964	c.1428delA	frameshift_variant	0.13	pyrazinamide
rpsA	1834975	c.1436delG	frameshift_variant	0.12	pyrazinamide
tlyA	1917795	c.-144delC	upstream_gene_variant	0.19	capreomycin
tlyA	1917889	c.-50delC	upstream_gene_variant	0.3	capreomycin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin
tlyA	1918194	c.255C>G	synonymous_variant	0.14	capreomycin
ndh	2102024	c.1018delG	frameshift_variant	0.19	ethionamide
ndh	2102024	c.1018delG	frameshift_variant	0.19	isoniazid
ndh	2102065	c.978delG	frameshift_variant	0.17	ethionamide
ndh	2102065	c.978delG	frameshift_variant	0.17	isoniazid
ndh	2102251	c.791delG	frameshift_variant	0.17	ethionamide
ndh	2102251	c.791delG	frameshift_variant	0.17	isoniazid
ndh	2102754	c.288delG	frameshift_variant	0.14	ethionamide
ndh	2102754	c.288delG	frameshift_variant	0.14	isoniazid
ndh	2102830	c.212delC	frameshift_variant	0.25	ethionamide
ndh	2102830	c.212delC	frameshift_variant	0.25	isoniazid
ndh	2102959	c.83dupA	frameshift_variant	0.25	ethionamide
ndh	2102959	c.83dupA	frameshift_variant	0.25	isoniazid
ndh	2103173	c.-133_-132insG	upstream_gene_variant	0.15	ethionamide
ndh	2103173	c.-133_-132insG	upstream_gene_variant	0.15	isoniazid
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Uncertain significance
katG	2156249	c.-139delG	upstream_gene_variant	0.17	isoniazid
katG	2156288	c.-178dupG	upstream_gene_variant	0.15	isoniazid
katG	2156335	c.-225delG	upstream_gene_variant	0.29	isoniazid
katG	2156370	c.-260delC	upstream_gene_variant	0.12	isoniazid
katG	2156445	c.-335delC	upstream_gene_variant	0.21	isoniazid
katG	2156454	c.-344delT	upstream_gene_variant	0.12	isoniazid
katG	2156470	c.-360delT	upstream_gene_variant	0.12	isoniazid
PPE35	2167825	c.2787delC	frameshift_variant	0.12	pyrazinamide
PPE35	2167916	c.2696dupT	frameshift_variant	0.2	pyrazinamide
PPE35	2167926	p.Leu896Ser	missense_variant	0.95	pyrazinamide	Uncertain significance
PPE35	2167955	c.2657dupG	frameshift_variant	0.13	pyrazinamide
PPE35	2168100	c.2512delC	frameshift_variant	0.15	pyrazinamide
PPE35	2168129	c.2483delC	frameshift_variant	0.36	pyrazinamide
PPE35	2168166	c.2446delA	frameshift_variant	0.43	pyrazinamide
PPE35	2168260	c.2352dupT	frameshift_variant	0.13	pyrazinamide
PPE35	2168428	c.2184delG	frameshift_variant	0.14	pyrazinamide
PPE35	2168461	c.2152delA	frameshift_variant	0.21	pyrazinamide
PPE35	2168678	c.1934delG	frameshift_variant	0.24	pyrazinamide
PPE35	2168852	c.1760dupC	frameshift_variant	0.14	pyrazinamide
PPE35	2168867	c.1744dupC	frameshift_variant	0.25	pyrazinamide
PPE35	2168880	c.1732_1733insT	frameshift_variant	0.18	pyrazinamide
PPE35	2168886	c.1726_1727insG	frameshift_variant	0.19	pyrazinamide
PPE35	2169178	c.1434dupC	frameshift_variant	0.17	pyrazinamide
PPE35	2169239	c.1373delC	frameshift_variant	0.3	pyrazinamide
PPE35	2169347	c.1265delT	frameshift_variant	0.19	pyrazinamide
PPE35	2169464	c.1148delA	frameshift_variant	0.2	pyrazinamide
PPE35	2169812	c.800delT	frameshift_variant	0.14	pyrazinamide
PPE35	2169820	c.792delC	frameshift_variant	0.21	pyrazinamide
PPE35	2170048	p.Leu189Val	missense_variant	0.15	pyrazinamide
PPE35	2170053	p.Thr187Ser	missense_variant	0.15	pyrazinamide
PPE35	2170066	c.546dupC	frameshift_variant	0.36	pyrazinamide
PPE35	2170096	p.Arg173Trp	missense_variant	0.15	pyrazinamide
PPE35	2170104	c.508delC	frameshift_variant	0.25	pyrazinamide
PPE35	2170146	c.466delT	frameshift_variant	0.19	pyrazinamide
PPE35	2170269	c.343dupT	frameshift_variant	0.12	pyrazinamide
PPE35	2170400	c.212delC	frameshift_variant	0.15	pyrazinamide
PPE35	2170459	c.153dupG	frameshift_variant	0.2	pyrazinamide
PPE35	2170811	c.-201delG	upstream_gene_variant	0.19	pyrazinamide
Rv1979c	2222282	c.882delC	frameshift_variant	0.29	clofazimine
Rv1979c	2222282	c.882delC	frameshift_variant	0.29	bedaquiline
Rv1979c	2222832	c.332_333insT	frameshift_variant	0.17	clofazimine
Rv1979c	2222832	c.332_333insT	frameshift_variant	0.17	bedaquiline
Rv1979c	2223172	c.-9delC	upstream_gene_variant	0.33	clofazimine
Rv1979c	2223172	c.-9delC	upstream_gene_variant	0.33	bedaquiline
Rv1979c	2223192	c.-29_-28insC	upstream_gene_variant	0.11	clofazimine
Rv1979c	2223192	c.-29_-28insC	upstream_gene_variant	0.11	bedaquiline
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Uncertain significance
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Uncertain significance
pncA	2289433	c.-193delG	upstream_gene_variant	0.27	pyrazinamide
pncA	2289651	c.-411delC	upstream_gene_variant	0.2	pyrazinamide
pncA	2289698	c.-458delT	upstream_gene_variant	0.12	pyrazinamide
pncA	2289763	c.-523dupT	upstream_gene_variant	0.15	pyrazinamide
pncA	2289824	c.-584delA	upstream_gene_variant	0.14	pyrazinamide
pncA	2289832	c.-592dupT	upstream_gene_variant	0.12	pyrazinamide
pncA	2289912	c.-672delT	upstream_gene_variant	0.23	pyrazinamide
kasA	2518722	c.610delG	frameshift_variant	0.26	isoniazid
kasA	2518819	c.707delG	frameshift_variant	0.19	isoniazid
kasA	2519151	c.1038dupG	frameshift_variant	0.13	isoniazid
kasA	2519227	c.1115delA	frameshift_variant	0.24	isoniazid
kasA	2519329	c.1217delG	frameshift_variant	0.12	isoniazid
kasA	2519358	c.1246delT	frameshift_variant	0.21	isoniazid
eis	2714133	c.1199delT	frameshift_variant	0.13	kanamycin
eis	2714133	c.1199delT	frameshift_variant	0.13	amikacin
eis	2714485	c.847dupC	frameshift_variant	0.18	kanamycin
eis	2714485	c.847dupC	frameshift_variant	0.18	amikacin
eis	2715055	c.277delC	frameshift_variant	0.2	kanamycin
eis	2715055	c.277delC	frameshift_variant	0.2	amikacin
eis	2715081	c.251dupT	frameshift_variant	0.2	kanamycin
eis	2715081	c.251dupT	frameshift_variant	0.2	amikacin
eis	2715272	c.60delC	frameshift_variant	0.24	kanamycin
eis	2715272	c.60delC	frameshift_variant	0.24	amikacin
eis	2715513	c.-182delC	upstream_gene_variant	0.17	kanamycin
eis	2715513	c.-182delC	upstream_gene_variant	0.17	amikacin
eis	2715580	c.-249delC	upstream_gene_variant	0.28	kanamycin
eis	2715580	c.-249delC	upstream_gene_variant	0.28	amikacin
ahpC	2725930	c.-261delG	upstream_gene_variant	0.14	isoniazid
ahpC	2726081	c.-111delG	upstream_gene_variant	0.14	isoniazid
ahpC	2726093	c.-99delA	upstream_gene_variant	0.23	isoniazid
ahpC	2726567	c.377delA	frameshift_variant	0.18	isoniazid
folC	2746528	c.1069_1070delGC	frameshift_variant	0.12	para-aminosalicylic_acid
folC	2746612	c.986delG	frameshift_variant	0.27	para-aminosalicylic_acid
folC	2746630	c.968delG	frameshift_variant	0.3	para-aminosalicylic_acid
folC	2746660	c.938dupT	frameshift_variant	0.28	para-aminosalicylic_acid
folC	2746842	c.756delC	frameshift_variant	0.19	para-aminosalicylic_acid
folC	2746890	c.708delT	frameshift_variant	0.14	para-aminosalicylic_acid
folC	2746955	c.643dupG	frameshift_variant	0.12	para-aminosalicylic_acid
folC	2747097	c.501delC	frameshift_variant	0.38	para-aminosalicylic_acid
folC	2747302	c.296delC	frameshift_variant	0.12	para-aminosalicylic_acid
folC	2747742	c.-145delA	upstream_gene_variant	0.11	para-aminosalicylic_acid
pepQ	2859414	c.1004delG	frameshift_variant	0.31	clofazimine
pepQ	2859414	c.1004delG	frameshift_variant	0.31	bedaquiline
pepQ	2859591	c.827_828insG	frameshift_variant	0.21	clofazimine
pepQ	2859591	c.827_828insG	frameshift_variant	0.21	bedaquiline
pepQ	2859601	c.817delG	frameshift_variant	0.12	clofazimine
pepQ	2859601	c.817delG	frameshift_variant	0.12	bedaquiline
pepQ	2859635	c.783delG	frameshift_variant	0.4	clofazimine
pepQ	2859635	c.783delG	frameshift_variant	0.4	bedaquiline
pepQ	2859745	c.673delC	frameshift_variant	0.12	clofazimine
pepQ	2859745	c.673delC	frameshift_variant	0.12	bedaquiline
pepQ	2860091	c.327delC	frameshift_variant	0.12	clofazimine
pepQ	2860091	c.327delC	frameshift_variant	0.12	bedaquiline
pepQ	2860332	c.86dupA	frameshift_variant	0.15	clofazimine
pepQ	2860332	c.86dupA	frameshift_variant	0.15	bedaquiline
pepQ	2860516	c.-100dupC	upstream_gene_variant	0.12	clofazimine
pepQ	2860516	c.-100dupC	upstream_gene_variant	0.12	bedaquiline
ribD	2986690	c.-148delG	upstream_gene_variant	0.36	para-aminosalicylic_acid
ribD	2987030	c.197delG	frameshift_variant	0.12	para-aminosalicylic_acid
ribD	2987110	c.275delG	frameshift_variant	0.27	para-aminosalicylic_acid
ribD	2987119	c.284delG	frameshift_variant	0.13	para-aminosalicylic_acid
ribD	2987213	c.376delC	frameshift_variant	0.12	para-aminosalicylic_acid
ribD	2987275	c.439delG	frameshift_variant	0.14	para-aminosalicylic_acid
ribD	2987316	c.480delC	frameshift_variant	0.14	para-aminosalicylic_acid
ribD	2987484	c.651delC	frameshift_variant	0.12	para-aminosalicylic_acid
Rv2752c	3064569	c.1623delG	frameshift_variant	0.21	rifampicin
Rv2752c	3064569	c.1623delG	frameshift_variant	0.21	isoniazid
Rv2752c	3064701	c.1490delT	frameshift_variant	0.52	rifampicin
Rv2752c	3064701	c.1490delT	frameshift_variant	0.52	isoniazid
Rv2752c	3064729	c.1462delG	frameshift_variant	0.53	rifampicin
Rv2752c	3064729	c.1462delG	frameshift_variant	0.53	isoniazid
Rv2752c	3064788	c.1403delT	frameshift_variant	0.13	rifampicin	Uncertain significance
Rv2752c	3064788	c.1403delT	frameshift_variant	0.13	isoniazid	Uncertain significance
Rv2752c	3064829	c.1362delC	frameshift_variant	0.22	rifampicin
Rv2752c	3064829	c.1362delC	frameshift_variant	0.22	isoniazid
Rv2752c	3064839	c.1352delG	frameshift_variant	0.2	rifampicin
Rv2752c	3064839	c.1352delG	frameshift_variant	0.2	isoniazid
Rv2752c	3065247	c.944delT	frameshift_variant	0.17	rifampicin
Rv2752c	3065247	c.944delT	frameshift_variant	0.17	isoniazid
Rv2752c	3065422	c.770delG	frameshift_variant	0.12	rifampicin
Rv2752c	3065422	c.770delG	frameshift_variant	0.12	isoniazid
Rv2752c	3065652	c.539delG	frameshift_variant	0.12	rifampicin
Rv2752c	3065652	c.539delG	frameshift_variant	0.12	isoniazid
Rv2752c	3065846	c.345dupA	frameshift_variant	0.14	rifampicin
Rv2752c	3065846	c.345dupA	frameshift_variant	0.14	isoniazid
Rv2752c	3066078	c.113delG	frameshift_variant	0.12	rifampicin
Rv2752c	3066078	c.113delG	frameshift_variant	0.12	isoniazid
Rv2752c	3066171	c.20dupC	frameshift_variant	0.15	rifampicin
Rv2752c	3066171	c.20dupC	frameshift_variant	0.15	isoniazid
Rv2752c	3066236	c.-46delC	upstream_gene_variant	0.27	rifampicin
Rv2752c	3066236	c.-46delC	upstream_gene_variant	0.27	isoniazid
Rv2752c	3066309	c.-119delG	upstream_gene_variant	0.17	rifampicin
Rv2752c	3066309	c.-119delG	upstream_gene_variant	0.17	isoniazid
Rv2752c	3067110	c.-920delG	upstream_gene_variant	0.17	rifampicin
Rv2752c	3067110	c.-920delG	upstream_gene_variant	0.17	isoniazid
Rv2752c	3067171	c.-982_-981insA	upstream_gene_variant	0.16	rifampicin
Rv2752c	3067171	c.-982_-981insA	upstream_gene_variant	0.16	isoniazid
thyX	3067273	c.672delC	frameshift_variant	0.14	para-aminosalicylic_acid
thyX	3067285	c.660delC	frameshift_variant	0.14	para-aminosalicylic_acid
thyX	3067401	c.544dupC	frameshift_variant	0.28	para-aminosalicylic_acid
thyX	3067567	c.378delC	frameshift_variant	0.28	para-aminosalicylic_acid
thyX	3067607	c.338delA	frameshift_variant	0.33	para-aminosalicylic_acid
thyX	3067961	c.-17delG	upstream_gene_variant	0.24	para-aminosalicylic_acid
thyX	3068081	c.-137_-136insT	upstream_gene_variant	0.18	para-aminosalicylic_acid
thyA	3074036	c.435delC	frameshift_variant	0.12	para-aminosalicylic_acid
thyA	3074283	c.187dupT	frameshift_variant	0.16	para-aminosalicylic_acid
thyA	3074573	c.-103delG	upstream_gene_variant	0.44	para-aminosalicylic_acid
ald	3086739	c.-81_-80insA	upstream_gene_variant	0.12	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
ald	3086955	c.138delC	frameshift_variant	0.15	cycloserine
ald	3086993	c.176delG	frameshift_variant	0.12	cycloserine
ald	3087000	c.183delC	frameshift_variant	0.12	cycloserine
ald	3087015	c.198delC	frameshift_variant	0.12	cycloserine
ald	3087278	c.464dupG	frameshift_variant	0.14	cycloserine
ald	3087506	c.690dupA	frameshift_variant	0.16	cycloserine
ald	3087807	c.991delG	frameshift_variant	0.46	cycloserine
ald	3087881	c.1063delG	frameshift_variant	0.12	cycloserine
ald	3087888	c.1071delC	frameshift_variant	0.24	cycloserine
fbiD	3339010	c.-107delA	upstream_gene_variant	0.14	delamanid
fbiD	3339323	c.208delG	frameshift_variant	0.15	delamanid
fbiD	3339362	c.248delC	frameshift_variant	0.22	delamanid
fbiD	3339381	c.267dupC	frameshift_variant	0.11	delamanid
fbiD	3339688	c.576dupC	frameshift_variant	0.17	delamanid
Rv3083	3448447	c.-57_-56insA	upstream_gene_variant	0.15	ethionamide
Rv3083	3448537	c.36delC	frameshift_variant	0.25	ethionamide
Rv3083	3448559	c.58delG	frameshift_variant	0.17	ethionamide
Rv3083	3448590	c.89delA	frameshift_variant	0.16	ethionamide
Rv3083	3448884	c.382delA	frameshift_variant	0.12	ethionamide
Rv3083	3449258	c.758delA	frameshift_variant	0.11	ethionamide
Rv3083	3449586	c.1085delG	frameshift_variant	0.2	ethionamide
Rv3083	3449614	c.1112delT	frameshift_variant	0.18	ethionamide
Rv3083	3449713	c.1212delC	frameshift_variant	0.54	ethionamide
Rv3083	3449881	c.1380delG	frameshift_variant	0.27	ethionamide
fprA	3473809	c.-197delA	upstream_gene_variant	0.11	capreomycin
fprA	3473809	c.-197delA	upstream_gene_variant	0.11	amikacin
fprA	3473850	c.-156delG	upstream_gene_variant	0.12	capreomycin
fprA	3473850	c.-156delG	upstream_gene_variant	0.12	amikacin
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0	capreomycin
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0	amikacin
fprA	3474044	c.39delG	frameshift_variant	0.19	capreomycin
fprA	3474044	c.39delG	frameshift_variant	0.19	amikacin
fprA	3474386	c.383delT	frameshift_variant	0.11	capreomycin
fprA	3474386	c.383delT	frameshift_variant	0.11	amikacin
fprA	3474443	c.440delG	frameshift_variant	0.3	capreomycin
fprA	3474443	c.440delG	frameshift_variant	0.3	amikacin
fprA	3474473	c.470dupA	frameshift_variant	0.16	capreomycin
fprA	3474473	c.470dupA	frameshift_variant	0.16	amikacin
fprA	3474968	c.964delG	frameshift_variant	0.17	capreomycin
fprA	3474968	c.964delG	frameshift_variant	0.17	amikacin
fprA	3475041	c.1037delG	frameshift_variant	0.14	capreomycin
fprA	3475041	c.1037delG	frameshift_variant	0.14	amikacin
fprA	3475171	c.1167delC	frameshift_variant	0.27	capreomycin
fprA	3475171	c.1167delC	frameshift_variant	0.27	amikacin
fprA	3475337	c.1333delG	frameshift_variant	0.36	capreomycin
fprA	3475337	c.1333delG	frameshift_variant	0.36	amikacin
fprA	3475374	c.1368_1369insG	frameshift_variant&stop_lost&splice_region_variant	0.25	capreomycin
fprA	3475374	c.1368_1369insG	frameshift_variant&stop_lost&splice_region_variant	0.25	amikacin
whiB7	3568427	c.251_252delGA	frameshift_variant	0.17	streptomycin
					kanamycin
					amikacin
whiB7	3568474	c.205dupG	frameshift_variant	0.14	streptomycin
					kanamycin
					amikacin
whiB7	3568611	c.68delG	frameshift_variant	0.25	streptomycin
					kanamycin
					amikacin
Rv3236c	3611983	c.1133delC	frameshift_variant	0.12	pyrazinamide
Rv3236c	3612113	c.1003delG	frameshift_variant	0.14	pyrazinamide	Uncertain significance
Rv3236c	3612674	c.442dupA	frameshift_variant	0.2	pyrazinamide
Rv3236c	3612813	p.Thr102Ala	missense_variant	1.0	pyrazinamide	Uncertain significance
Rv3236c	3612817	c.299delA	frameshift_variant	0.26	pyrazinamide
Rv3236c	3612904	c.212dupT	frameshift_variant	0.12	pyrazinamide
Rv3236c	3612994	c.122delT	frameshift_variant	0.12	pyrazinamide
fbiA	3640651	c.111delC	frameshift_variant	0.15	delamanid
fbiA	3640677	c.137delA	frameshift_variant	0.28	delamanid
fbiA	3640683	c.143delG	frameshift_variant	0.12	delamanid
fbiA	3641023	c.482dupA	frameshift_variant	0.12	delamanid
fbiA	3641187	c.647delC	frameshift_variant	0.12	delamanid
fbiA	3641265	c.725delG	frameshift_variant	0.3	delamanid
fbiA	3641287	c.749dupA	frameshift_variant	0.14	delamanid
fbiA	3641420	c.878delG	frameshift_variant	0.12	delamanid
fbiA	3641439	c.901dupG	frameshift_variant	0.11	delamanid
fbiA	3641456	c.916delG	frameshift_variant	0.11	delamanid
fbiB	3641850	c.318delC	frameshift_variant	0.37	delamanid
fbiB	3642827	c.1295delC	frameshift_variant	0.3	delamanid
fbiB	3642844	c.1313delC	frameshift_variant	0.2	delamanid
alr	3840314	c.1106delG	frameshift_variant	0.31	cycloserine
alr	3840326	c.1094dupT	frameshift_variant	0.12	cycloserine
alr	3840775	c.645dupT	frameshift_variant	0.12	cycloserine
alr	3840937	c.483delG	frameshift_variant	0.12	cycloserine
alr	3841306	c.114delC	frameshift_variant	0.2	cycloserine
rpoA	3877509	c.999delG	frameshift_variant	0.16	rifampicin
rpoA	3877794	c.713delC	frameshift_variant	0.38	rifampicin
rpoA	3877830	c.677delA	frameshift_variant	0.19	rifampicin
rpoA	3877960	p.Val183Gly	missense_variant	1.0	rifampicin
rpoA	3878077	c.430delC	frameshift_variant	0.11	rifampicin
rpoA	3878311	c.196delG	frameshift_variant	0.19	rifampicin
rpoA	3878490	c.18delC	frameshift_variant	0.12	rifampicin
rpoA	3878527	c.-21delT	upstream_gene_variant	0.17	rifampicin
rpoA	3878691	c.-185dupC	upstream_gene_variant	0.13	rifampicin
ddn	3987149	c.311dupA	frameshift_variant	0.19	delamanid
ddn	3987177	c.337delG	frameshift_variant	0.24	delamanid
ddn	3987210	c.369delG	frameshift_variant	0.16	delamanid
clpC1	4038278	c.2426delG	frameshift_variant	0.21	pyrazinamide
clpC1	4038372	c.2332delC	frameshift_variant	0.14	pyrazinamide
clpC1	4038595	c.2109dupA	frameshift_variant	0.11	pyrazinamide
clpC1	4038712	c.1992delT	frameshift_variant	0.12	pyrazinamide
clpC1	4038851	c.1853delC	frameshift_variant	0.11	pyrazinamide
clpC1	4039249	c.1455delC	frameshift_variant	0.15	pyrazinamide
clpC1	4039655	c.1049delC	frameshift_variant	0.16	pyrazinamide
clpC1	4039849	c.855dupT	frameshift_variant	0.11	pyrazinamide
clpC1	4039943	c.761delC	frameshift_variant	0.13	pyrazinamide
clpC1	4040232	c.472delC	frameshift_variant	0.14	pyrazinamide
clpC1	4040256	c.448delG	frameshift_variant	0.17	pyrazinamide
clpC1	4040447	c.257dupA	frameshift_variant	0.2	pyrazinamide
clpC1	4040457	c.247delC	frameshift_variant	0.19	pyrazinamide
clpC1	4040600	c.104dupT	frameshift_variant	0.12	pyrazinamide
panD	4043878	c.403dupC	frameshift_variant	0.18	pyrazinamide
panD	4043901	c.380dupA	frameshift_variant	0.18	pyrazinamide
panD	4043997	c.284delA	frameshift_variant	0.17	pyrazinamide
panD	4044034	c.247dupG	frameshift_variant	0.12	pyrazinamide
panD	4044191	c.90delC	frameshift_variant	0.14	pyrazinamide
panD	4044210	c.71delG	frameshift_variant	0.44	pyrazinamide
embC	4239927	c.68delG	frameshift_variant	0.15	ethambutol
embC	4240049	c.191dupA	frameshift_variant	0.18	ethambutol
embC	4240451	c.590delT	frameshift_variant	0.11	ethambutol
embC	4240570	c.712dupG	frameshift_variant	0.13	ethambutol
embC	4240782	c.923delG	frameshift_variant	0.24	ethambutol
embC	4241323	c.1464dupT	frameshift_variant	0.17	ethambutol
embC	4241446	c.1586delG	frameshift_variant	0.14	ethambutol
embC	4241606	c.1748dupC	frameshift_variant	0.13	ethambutol
embC	4241632	c.1774dupG	frameshift_variant	0.11	ethambutol
embC	4241643	c.1785dupG	frameshift_variant	0.12	ethambutol
embC	4241985	c.2125delG	frameshift_variant	0.12	ethambutol
embC	4242011	c.2153dupT	frameshift_variant	0.12	ethambutol
embC	4242188	c.2329delC	frameshift_variant	0.41	ethambutol
embC	4242275	c.2413delG	frameshift_variant	0.2	ethambutol
embC	4242285	c.2423delT	frameshift_variant	0.14	ethambutol
embC	4242430	c.2570delG	frameshift_variant	0.14	ethambutol
embC	4242591	c.2731delC	frameshift_variant	0.12	ethambutol
embC	4242598	c.2739delG	frameshift_variant	0.18	ethambutol
embC	4242617	c.2756delA	frameshift_variant	0.17	ethambutol
embA	4242643	c.-590C>T	upstream_gene_variant	1.0	ethambutol
embC	4242910	c.3050delG	frameshift_variant	0.4	ethambutol
embA	4243185	c.-47delC	upstream_gene_variant	0.16	ethambutol
embA	4243460	c.228C>T	synonymous_variant	0.97	ethambutol
embA	4243606	c.376delG	frameshift_variant	0.13	ethambutol
embA	4243680	c.449delC	frameshift_variant	0.11	ethambutol
embA	4243755	c.525delC	frameshift_variant	0.12	ethambutol
embA	4243823	c.592delA	frameshift_variant	0.13	ethambutol
embA	4243881	c.651delC	frameshift_variant	0.41	ethambutol
embA	4244189	c.962delG	frameshift_variant	0.13	ethambutol
embA	4244544	c.1314delC	frameshift_variant	0.25	ethambutol
embA	4244631	c.1401delC	frameshift_variant	0.23	ethambutol
embA	4244701	c.1472delC	frameshift_variant	0.17	ethambutol
embA	4244850	c.1621delG	frameshift_variant	0.2	ethambutol
embA	4245113	c.1883delG	frameshift_variant	0.14	ethambutol
embA	4245128	c.1898delC	frameshift_variant	0.26	ethambutol
embA	4245179	c.1950dupT	frameshift_variant	0.11	ethambutol
embA	4245828	c.2598delG	frameshift_variant	0.16	ethambutol
embA	4246038	c.2808delC	frameshift_variant	0.11	ethambutol
embA	4246112	c.2881_2882insC	frameshift_variant	0.18	ethambutol
embA	4246223	c.2993delG	frameshift_variant	0.56	ethambutol
embA	4246392	c.3164dupG	frameshift_variant	0.2	ethambutol
embA	4246503	c.3274delG	frameshift_variant	0.23	ethambutol
embA	4246514	c.3282_3283insC	frameshift_variant&stop_lost&splice_region_variant	0.19	ethambutol
embB	4246531	c.19delA	frameshift_variant	0.15	ethambutol
embB	4246547	c.35_36delCA	frameshift_variant	0.12	ethambutol
embB	4246563	c.55dupG	frameshift_variant	0.2	ethambutol
embB	4246624	c.114delT	frameshift_variant	0.12	ethambutol
embB	4246694	c.186dupG	frameshift_variant	0.15	ethambutol
embB	4246747	c.237dupT	frameshift_variant	0.13	ethambutol
embB	4246830	c.318delC	frameshift_variant	0.16	ethambutol
embB	4247016	c.506dupG	frameshift_variant	0.35	ethambutol
embB	4247051	c.537dupC	frameshift_variant	0.17	ethambutol
embB	4247076	c.564dupG	frameshift_variant	0.13	ethambutol
embB	4247081	c.570delC	frameshift_variant	0.21	ethambutol
embB	4247282	c.771delG	frameshift_variant	0.26	ethambutol
embB	4247354	c.843delC	frameshift_variant	0.32	ethambutol
embB	4247503	c.992delG	frameshift_variant	0.16	ethambutol
embB	4247637	c.1126delG	frameshift_variant	0.13	ethambutol
embB	4247792	c.1281delG	frameshift_variant	0.14	ethambutol
embB	4248043	c.1534delA	frameshift_variant	0.14	ethambutol
embB	4248548	c.2037delC	frameshift_variant	0.19	ethambutol
embB	4248739	c.2229dupT	frameshift_variant	0.22	ethambutol
embB	4248798	c.2288delT	frameshift_variant	0.28	ethambutol
embB	4248871	c.2360delG	frameshift_variant	0.21	ethambutol
embB	4249061	c.2550delC	frameshift_variant	0.12	ethambutol
embB	4249340	c.2829delC	frameshift_variant	0.11	ethambutol
embB	4249403	c.2894delC	frameshift_variant	0.14	ethambutol
embB	4249535	c.3025delA	frameshift_variant	0.15	ethambutol
embB	4249631	c.3120delC	frameshift_variant	0.14	ethambutol
aftB	4267432	c.1404delC	frameshift_variant	0.44	capreomycin
aftB	4267432	c.1404delC	frameshift_variant	0.44	amikacin
aftB	4267579	c.1257delG	frameshift_variant	0.21	capreomycin
aftB	4267579	c.1257delG	frameshift_variant	0.21	amikacin
aftB	4267647	p.Asp397Gly	missense_variant	1.0	capreomycin	Uncertain significance
aftB	4267647	p.Asp397Gly	missense_variant	1.0	amikacin	Uncertain significance
aftB	4267693	c.1142dupG	frameshift_variant	0.16	capreomycin
aftB	4267693	c.1142dupG	frameshift_variant	0.16	amikacin
aftB	4267769	c.1067delT	frameshift_variant	0.14	capreomycin
aftB	4267769	c.1067delT	frameshift_variant	0.14	amikacin
aftB	4267837	c.999dupT	frameshift_variant	0.12	capreomycin
aftB	4267837	c.999dupT	frameshift_variant	0.12	amikacin
aftB	4267959	p.Val293Ala	missense_variant	0.11	capreomycin
aftB	4267959	p.Val293Ala	missense_variant	0.11	amikacin
aftB	4267960	c.876delC	frameshift_variant	0.14	capreomycin
aftB	4267960	c.876delC	frameshift_variant	0.14	amikacin
aftB	4267978	c.858delG	frameshift_variant	0.18	capreomycin
aftB	4267978	c.858delG	frameshift_variant	0.18	amikacin
aftB	4268274	c.562delG	frameshift_variant	0.11	capreomycin
aftB	4268274	c.562delG	frameshift_variant	0.11	amikacin
aftB	4268482	c.354delT	frameshift_variant	0.12	capreomycin
aftB	4268482	c.354delT	frameshift_variant	0.12	amikacin
aftB	4268575	c.261delC	frameshift_variant	0.14	capreomycin
aftB	4268575	c.261delC	frameshift_variant	0.14	amikacin
aftB	4268776	c.60dupG	frameshift_variant	0.14	capreomycin
aftB	4268776	c.60dupG	frameshift_variant	0.14	amikacin
ubiA	4269157	c.677delC	frameshift_variant	0.11	ethambutol
ubiA	4269303	c.530delT	frameshift_variant	0.3	ethambutol
ubiA	4269344	p.Gly164Arg	missense_variant	0.12	ethambutol
ubiA	4269346	p.Ala163Gly	missense_variant	0.15	ethambutol
ubiA	4269747	c.86dupA	frameshift_variant	0.25	ethambutol
ubiA	4269788	c.45delC	frameshift_variant	0.12	ethambutol
ubiA	4269854	c.-28delG	upstream_gene_variant	0.17	ethambutol
ubiA	4269899	c.-67delC	upstream_gene_variant	0.18	ethambutol
ubiA	4270024	c.-192delC	upstream_gene_variant	0.21	ethambutol
ethA	4326676	p.Ser266Arg	missense_variant	1.0	ethionamide	Uncertain significance
ethA	4326699	c.766_774delTGGCCACGG	conservative_inframe_deletion	1.0	ethionamide
ethR	4327605	c.59delC	frameshift_variant	0.15	ethionamide
ethR	4327728	c.182delT	frameshift_variant	0.22	ethionamide
ethR	4328046	c.500delC	frameshift_variant	0.14	ethionamide
ethA	4328437	c.-965delC	upstream_gene_variant	0.35	ethionamide
whiB6	4338323	c.198delC	frameshift_variant	0.14	streptomycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	streptomycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
whiB6	4338676	c.-156delG	upstream_gene_variant	0.23	streptomycin	Uncertain significance
					capreomycin
					amikacin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin
gid	4407599	c.603delC	frameshift_variant	0.22	streptomycin
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Uncertain significance
gid	4408360	c.-159delA	upstream_gene_variant	0.13	streptomycin