TB-Profiler

TB-Profiler result

Run: SRR3675272

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: SRR3675272

Sample name:

Date: 2024-10-04T05:59:43.635999

Number of reads: 288736

Percentage reads mapped: 98.88

Median coverage: 8.0

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	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
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
mmpL5	778537	c.-57G>A	upstream_gene_variant	1.0	bedaquiline
mmpL5	778537	c.-57G>A	upstream_gene_variant	1.0	clofazimine
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1473666	n.9G>A	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1473666	n.9G>A	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1475008	n.1351C>A	non_coding_transcript_exon_variant	0.95	capreomycin	Uncertain significance
rrl	1475008	n.1351C>A	non_coding_transcript_exon_variant	0.95	linezolid	Uncertain significance
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
pncA	2289365	c.-125delC	upstream_gene_variant	1.0	pyrazinamide
ahpC	2726105	c.-88G>A	upstream_gene_variant	1.0	isoniazid	Not assoc w R
Rv2477c	2782498	c.1545C>T	synonymous_variant	1.0	kanamycin	Not assoc w R
					levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					rifampicin	Not assoc w R
					ethambutol	Not assoc w R
					amikacin	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
embB	4249456	c.2943G>A	synonymous_variant	1.0	ethambutol
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin