TB-Profiler

TB-Profiler result

Run: ERR4816192

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: ERR4816192

Sample name:

Date: 2024-04-15T04:36:36.217128

Number of reads: 581950

Percentage reads mapped: 98.52

Median coverage: 10.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON

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	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	9596	c.2295G>T	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrA	9596	c.2295G>T	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
fgd1	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Not assoc w R - Interim
nusG	734354	p.Pro34Leu	missense_variant	1.0	rifampicin	Not assoc w R
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	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
pncA	2289047	c.195C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
pncA	2289365	c.-125delC	upstream_gene_variant	1.0	pyrazinamide
eis	2715432	c.-100C>T	upstream_gene_variant	1.0	amikacin
eis	2715432	c.-100C>T	upstream_gene_variant	1.0	kanamycin
ahpC	2726105	c.-88G>A	upstream_gene_variant	1.0	isoniazid	Not assoc w R
Rv2477c	2782498	c.1545C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					levofloxacin	Not assoc w R
					kanamycin	Not assoc w R
					rifampicin	Not assoc w R
					amikacin	Not assoc w R
pepQ	2859359	p.Thr354Ala	missense_variant	1.0	clofazimine	Uncertain significance
pepQ	2859359	p.Thr354Ala	missense_variant	1.0	bedaquiline	Uncertain significance
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
ethA	4328270	c.-797C>T	upstream_gene_variant	1.0	ethionamide
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin