TB-Profiler

TB-Profiler result

Run: SRR6045796

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: SRR6045796

Sample name:

Date: 2024-04-15T00:59:56.184617

Number of reads: 388707

Percentage reads mapped: 50.37

Median coverage: 10.0

Strain: lineage3.1.2

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	0.99
lineage3.1.2	East-African-Indian	RD750	1.0
lineage3.1	East-African-Indian	RD750	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	katG	p.Ser315Thr	Assoc w R	High-level resistance
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
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance

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
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
rpoB	759746	c.-61C>T	upstream_gene_variant	1.0	rifampicin	Not assoc w R
rpoB	762434	c.2628T>G	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1129c	1254562	c.-28T>C	upstream_gene_variant	1.0	moxifloxacin	Not assoc w R
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
Rv1258c	1406242	p.Ala367Thr	missense_variant	1.0	streptomycin	Uncertain significance
					isoniazid	Uncertain significance
					pyrazinamide	Uncertain significance
embR	1416676	c.672G>A	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1918104	c.165G>A	synonymous_variant	1.0	capreomycin	Not assoc w R - Interim
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
pncA	2289047	c.195C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embC	4242075	p.Arg738Gln	missense_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338494	p.Thr10Ala	missense_variant	1.0	capreomycin	Uncertain significance
					amikacin	Uncertain significance
					kanamycin	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407956	p.Arg83Gly	missense_variant	1.0	streptomycin	Uncertain significance