TB-Profiler

TB-Profiler result

Run: SRR11972180

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: SRR11972180

Sample name:

Date: 2025-02-11T14:49:10.534765

Number of reads: 381743

Percentage reads mapped: 99.4

Median coverage: 6.0

Strain: lineage2.2.1.1;lineage4

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	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	0.5
lineage4	Euro-American	None	0.69
lineage2.2.1.1	East-Asian (Beijing)	RD105;RD207;RD181;RD150	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
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
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance

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
rpoC	765822	p.Ala818Val	missense_variant	1.0	rifampicin	Uncertain significance
Rv1258c	1406760	c.580_581insC	frameshift_variant	1.0	streptomycin	Uncertain significance
					pyrazinamide	Uncertain significance
					isoniazid	Uncertain significance
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	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
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R