TB-Profiler

TB-Profiler result

Run: ERR1213843

Summary

Run ID: ERR1213843

Sample name:

Date: 2025-06-05T14:48:41.990016

Number of reads: 4910329

Percentage reads mapped: 99.57

Median coverage: 97.0

Strain: lineage4

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid	ahpC	c.-52C>T	Uncertain significance	Mutation from literature
ethambutol	embB	p.Gly406Asp	Assoc w R
ethambutol	embB	p.Asp1024Asn	Uncertain significance	Mutation from literature
pyrazinamide	pncA	p.Thr76Pro	Assoc w R
streptomycin	gid	p.Glu173*	Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	ethA	p.Cys131*	Assoc w R
clofazimine
para-aminosalicylic_acid	folC	p.Ile43Thr		Mutation from literature
delamanid
bedaquiline
linezolid

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	Comment
pncA	2289016	p.Thr76Pro	missense_variant	1.0	pyrazinamide	Assoc w R
ahpC	2726141	c.-52C>T	upstream_gene_variant	1.0	isoniazid	Uncertain significance	Mutation from literature
folC	2747471	p.Ile43Thr	missense_variant	1.0	para-aminosalicylic_acid		Mutation from literature
embB	4247730	p.Gly406Asp	missense_variant	1.0	ethambutol	Assoc w R
embB	4249583	p.Asp1024Asn	missense_variant	1.0	ethambutol	Uncertain significance	Mutation from literature
ethA	4327081	p.Cys131*	stop_gained	1.0	ethionamide	Assoc w R
gid	4407686	p.Glu173*	stop_gained	0.99	streptomycin	Assoc w R

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
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
gyrA	8147	p.Asn282Lys	missense_variant	1.0	levofloxacin	Uncertain significance
gyrA	8147	p.Asn282Lys	missense_variant	1.0	moxifloxacin	Uncertain significance
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
Rv0010c	13571	c.-13G>C	upstream_gene_variant	1.0	isoniazid	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	0.99	streptomycin	Not assoc w R
fbiC	1304501	p.Ala524Gly	missense_variant	1.0	clofazimine	Uncertain significance
					delamanid	Uncertain significance
					pretomanid	Uncertain significance
fbiC	1305357	c.2427C>G	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
					delamanid	Not assoc w R - Interim
					pretomanid	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	amikacin	Uncertain significance
					capreomycin	Uncertain significance
					kanamycin	Uncertain significance
					streptomycin	Uncertain significance
tsnR	1854300	p.Leu232Pro	missense_variant	0.96	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
katG	2154277	p.Asp612Gly	missense_variant	1.0	isoniazid	Uncertain significance
katG	2155141	p.Thr324Leu	missense_variant	1.0	isoniazid	Uncertain significance
PPE35	2168742	p.Gly624Asp	missense_variant	1.0	pyrazinamide	Uncertain significance
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
pncA	2290088	c.-847G>A	upstream_gene_variant	1.0	pyrazinamide	Uncertain significance
eis	2715660	c.-328C>T	upstream_gene_variant	1.0	amikacin	Uncertain significance
eis	2715660	c.-328C>T	upstream_gene_variant	1.0	kanamycin	Uncertain significance
Rv2752c	3065482	p.Cys237Tyr	missense_variant	1.0	ethambutol	Uncertain significance
					isoniazid	Uncertain significance
					levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					rifampicin	Uncertain significance
Rv3236c	3612113	c.1003dupG	frameshift_variant	1.0	pyrazinamide	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4246401	p.Val1057Met	missense_variant	1.0	ethambutol	Uncertain significance
embB	4247675	p.Ala388Thr	missense_variant	1.0	ethambutol	Uncertain significance
ethA	4327376	p.Ala33Gly	missense_variant	1.0	ethionamide	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	amikacin	Not assoc w R
					capreomycin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	amikacin	Uncertain significance
					capreomycin	Uncertain significance
					kanamycin	Uncertain significance