TB-Profiler

TB-Profiler result

Run: ERR13290151

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: ERR13290151

Sample name:

Date: 2025-02-11T11:42:40.922779

Number of reads: 407113

Percentage reads mapped: 99.63

Median coverage: 13.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	1.0
lineage4.1.2	Euro-American	None	1.0
lineage4.1.2.1	Euro-American (Haarlem)	RD182	1.0
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
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
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

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	7425	p.Pro42Ser	missense_variant	1.0	levofloxacin
gyrA	7425	p.Pro42Ser	missense_variant	1.0	moxifloxacin
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
fgd1	491591	p.Lys270Met	missense_variant	1.0	pretomanid
					delamanid	Uncertain significance
					clofazimine	Not assoc w R
ccsA	620836	p.Gly316Cys	missense_variant	1.0	kanamycin
					capreomycin
					amikacin
rpoB	760106	c.300G>A	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoB	760115	c.309C>T	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
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	781276	c.-284A>C	upstream_gene_variant	1.0	streptomycin
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1254583	c.-49A>C	upstream_gene_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Not assoc w R
					rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2169827	c.786G>A	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
kasA	2518076	c.-39C>T	upstream_gene_variant	1.0	isoniazid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
fbiA	3641454	c.912G>A	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R - Interim
embC	4239298	c.-565C>T	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embC	4242803	p.Val981Leu	missense_variant	1.0	ethambutol	Not assoc w R