TB-Profiler

TB-Profiler result

Run: SRR5535715

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: SRR5535715

Sample name:

Date: 2024-04-15T12:55:30.326104

Number of reads: 1600028

Percentage reads mapped: 98.85

Median coverage: 25.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	0.99
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	1.0
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	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin	gyrB	p.Asp494Ala	Uncertain significance	Mutation from literature
ofloxacin
levofloxacin	gyrB	p.Asp494Ala	Uncertain significance	Mutation from literature
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid	folC	p.Ile43Thr		Mutation from literature
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
gyrB	6720	p.Asp494Ala	missense_variant	1.0	levofloxacin	Uncertain significance	Mutation from literature
gyrB	6720	p.Asp494Ala	missense_variant	1.0	moxifloxacin	Uncertain significance	Mutation from literature
katG	2155168	p.Ser315Thr	missense_variant	0.93	isoniazid	Assoc w R	High-level resistance
folC	2747471	p.Ile43Thr	missense_variant	1.0	para-aminosalicylic_acid		Mutation from literature

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
mshA	575907	p.Ala187Val	missense_variant	1.0	ethionamide	Not assoc w R
mshA	575907	p.Ala187Val	missense_variant	1.0	isoniazid	Not assoc w R
ccsA	620625	p.Ile245Met	missense_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Uncertain significance
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
Rv0565c	657142	p.Arg110His	missense_variant	1.0	ethionamide	Uncertain significance
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
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
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
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	bedaquiline	Not assoc w R
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
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
rrs	1471647	n.-199G>C	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rpsA	1834177	c.636A>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	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
fbiD	3338889	c.-229T>C	upstream_gene_variant	1.0	clofazimine
					pretomanid
					delamanid
Rv3236c	3612813	p.Thr102Ala	missense_variant	1.0	pyrazinamide	Not assoc w R - Interim
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4243460	c.228C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338365	p.Cys53Arg	missense_variant	1.0	capreomycin	Uncertain significance
					amikacin	Uncertain significance
					kanamycin	Uncertain significance
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	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
gid	4407588	c.615A>G	synonymous_variant	0.96	streptomycin	Not assoc w R
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R