TB-Profiler

TB-Profiler result

Run: ERR2704709

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: ERR2704709

Sample name:

Date: 2025-02-11T10:06:42.677476

Number of reads: 1397651

Percentage reads mapped: 99.56

Median coverage: 24.0

Strain: lineage4.2.1.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.2	Euro-American	None	1.0
lineage4	Euro-American	None	1.0
lineage4.2.1.1	Euro-American (TUR)	None	1.0
lineage4.2.1	Euro-American (TUR)	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	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	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
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
mmpL5	777451	p.Val344Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	777451	p.Val344Leu	missense_variant	1.0	clofazimine	Uncertain significance
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rplC	800204	c.-605T>C	upstream_gene_variant	1.0	linezolid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
bacA	2063685	c.1044G>A	synonymous_variant	1.0	kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					amikacin	Not assoc w R
PPE35	2170813	c.-201G>C	upstream_gene_variant	1.0	pyrazinamide
Rv2752c	3064701	p.Phe497Leu	missense_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
					ethambutol
ald	3086742	c.-78A>C	upstream_gene_variant	1.0	cycloserine
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
ddn	3987092	p.Glu83Asp	missense_variant	1.0	pretomanid
ddn	3987092	p.Glu83Asp	missense_variant	1.0	delamanid	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
gid	4408213	c.-11C>T	upstream_gene_variant	1.0	streptomycin	Uncertain significance