TB-Profiler

TB-Profiler result

Run: SRR29017330

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: SRR29017330

Sample name:

Date: 2025-02-11T16:56:15.064281

Number of reads: 306086

Percentage reads mapped: 99.49

Median coverage: 7.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage4.3	Euro-American (LAM)	None	1.0
lineage4	Euro-American	None	1.0
lineage4.3.3	Euro-American (LAM)	RD115	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.Thr380Ile	Uncertain significance	Mutation from literature
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	2154973	p.Thr380Ile	missense_variant	1.0	isoniazid	Uncertain significance	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	8040	p.Gly247Ser	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	8040	p.Gly247Ser	missense_variant	1.0	moxifloxacin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
katG	2155211	p.Lys301Glu	missense_variant	0.85	isoniazid
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	4408156	p.Leu16Arg	missense_variant	1.0	streptomycin	Not assoc w R