TB-Profiler

TB-Profiler result

Run: DRR034407

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: DRR034407

Sample name:

Date: 2024-04-15T15:48:27.514831

Number of reads: 201207

Percentage reads mapped: 99.47

Median coverage: 6.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	0.98
lineage2.2	East-Asian (Beijing)	RD105;RD207	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
fgd1	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	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
fbiC	1302712	c.-219G>A	upstream_gene_variant	1.0	clofazimine
					pretomanid
					delamanid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrl	1473632	n.-26G>A	upstream_gene_variant	1.0	capreomycin	Uncertain significance
rrl	1473632	n.-26G>A	upstream_gene_variant	1.0	linezolid
inhA	1674693	c.492C>T	synonymous_variant	1.0	ethionamide
inhA	1674693	c.492C>T	synonymous_variant	1.0	isoniazid
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R