TB-Profiler

TB-Profiler result

Run: ERR2513853

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: ERR2513853

Sample name:

Date: 2024-04-15T06:37:50.723174

Number of reads: 1293988

Percentage reads mapped: 99.47

Median coverage: 26.0

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
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
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
pncA	2289365	c.-125delC	upstream_gene_variant	1.0	pyrazinamide
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
alr	3841473	c.-53G>A	upstream_gene_variant	1.0	cycloserine
panD	4044872	c.-591C>T	upstream_gene_variant	1.0	pyrazinamide
glpK	4138622	c.1134C>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
					rifampicin	Not assoc w R
					isoniazid	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