TB-Profiler

TB-Profiler result

Run: SRR11972234

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: SRR11972234

Sample name:

Date: 2024-04-15T19:38:28.661555

Number of reads: 191741

Percentage reads mapped: 99.32

Median coverage: 6.0

Strain: lineage1.2.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage1.2.1.2	Indo-Oceanic	RD239	0.52
lineage1	Indo-Oceanic	RD239	0.5
lineage1.2.1.2.1	Indo-Oceanic	RD239	0.52
lineage1.2.1	Indo-Oceanic	RD239	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
Rv0010c	13460	c.99T>C	synonymous_variant	1.0	isoniazid	Not assoc w R
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	763531	c.162G>C	synonymous_variant	1.0	rifampicin	Not assoc w R
embR	1417019	p.Cys110Tyr	missense_variant	1.0	ethambutol	Not assoc w R
embR	1417554	c.-207C>G	upstream_gene_variant	1.0	ethambutol
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
bacA	2062922	p.Ile603Val	missense_variant	1.0	streptomycin	Not assoc w R
					kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
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
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
whiB7	3568488	c.191delG	frameshift_variant	1.0	streptomycin	Uncertain significance
					amikacin	Uncertain significance
					kanamycin	Uncertain significance
embB	4247578	c.1065G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4247646	p.Glu378Ala	missense_variant	1.0	ethambutol	Not assoc w R
ubiA	4269606	c.228T>C	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269864	c.-32delG	upstream_gene_variant	1.0	ethambutol	Not assoc w R
whiB6	4338361	p.Arg54Gln	missense_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	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	4338603	c.-82C>T	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