TB-Profiler

TB-Profiler result

Run: ERR4817066

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: ERR4817066

Sample name:

Date: 2024-04-15T16:25:50.148559

Number of reads: 459812

Percentage reads mapped: 99.57

Median coverage: 9.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage3	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
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	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
mshA	575283	c.-65C>G	upstream_gene_variant	1.0	ethionamide	Uncertain significance
mshA	575283	c.-65C>G	upstream_gene_variant	1.0	isoniazid	Uncertain significance
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
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
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1253566	c.969A>G	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
					levofloxacin	Not assoc w R - Interim
					rifampicin	Not assoc w R
					isoniazid	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
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
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
pncA	2289047	c.195C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
ahpC	2726105	c.-88G>A	upstream_gene_variant	1.0	isoniazid	Not assoc w R
ahpC	2726111	c.-82T>A	upstream_gene_variant	1.0	isoniazid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
whiB7	3568857	c.-178C>T	upstream_gene_variant	1.0	streptomycin	Uncertain significance
					amikacin	Not assoc w R - Interim
					kanamycin	Not assoc w R - Interim
panD	4044023	c.259C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
panD	4044872	c.-591C>T	upstream_gene_variant	1.0	pyrazinamide
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	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