TB-Profiler

TB-Profiler result

Run: SRR6797640

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: SRR6797640

Sample name:

Date: 2024-10-05T09:42:32.482825

Number of reads: 900477

Percentage reads mapped: 99.57

Median coverage: 16.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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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	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	0.99

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin	rpoB	p.Ser450Leu	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Leu	Assoc w R
pyrazinamide	pncA	c.309_*1123del	Assoc w R
streptomycin	rpsL	p.Lys43Arg	Assoc w R
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
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
rpsL	781687	p.Lys43Arg	missense_variant	1.0	streptomycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2287557	c.309_*1123del	frameshift_variant&stop_lost&splice_region_variant	1.0	pyrazinamide	Assoc w R
embB	4247429	p.Met306Leu	missense_variant	1.0	ethambutol	Assoc w R

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
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
fgd1	491742	c.960T>C	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R
mshA	575907	p.Ala187Val	missense_variant	1.0	isoniazid	Not assoc w R
mshA	575907	p.Ala187Val	missense_variant	1.0	ethionamide	Not assoc w R
ccsA	620625	p.Ile245Met	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
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
rpoC	763501	p.Asp44Glu	missense_variant	1.0	rifampicin	Uncertain significance
rpoC	764841	p.Ile491Asn	missense_variant	1.0	rifampicin	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	bedaquiline	Not assoc w R
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	clofazimine	Not assoc w R
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
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	levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					isoniazid	Not assoc w R
					rifampicin	Not assoc w R
Rv1258c	1406760	c.580_581insC	frameshift_variant	1.0	streptomycin	Uncertain significance
					pyrazinamide	Uncertain significance
					isoniazid	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rpsA	1834177	c.636A>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
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	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv2752c	3066237	c.-47_-46delCCinsTT	upstream_gene_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
					ethambutol
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
mtrB	3626562	p.Pro18Ser	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3626562	p.Pro18Ser	missense_variant	1.0	bedaquiline	Uncertain significance
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	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R