TB-Profiler

TB-Profiler result

Run: SRR29016993

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: SRR29016993

Sample name:

Date: 2025-02-11T12:41:35.808553

Number of reads: 378882

Percentage reads mapped: 99.4

Median coverage: 12.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: RR-TB

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.8	Euro-American (mainly T)	RD219	0.97

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

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin	rpoB	p.Ser450Leu	Assoc w R
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
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	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	8424	c.1123C>A	synonymous_variant	1.0	levofloxacin
gyrA	8424	c.1123C>A	synonymous_variant	1.0	moxifloxacin
Rv0010c	13791	c.-233C>A	upstream_gene_variant	1.0	isoniazid
rpoB	761461	p.Arg552His	missense_variant	1.0	rifampicin	Uncertain significance
rpoB	762092	p.Glu762Asp	missense_variant	1.0	rifampicin
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
atpE	1460852	c.-193C>A	upstream_gene_variant	0.92	bedaquiline
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	linezolid	Not assoc w R
katG	2156601	c.-490T>C	upstream_gene_variant	1.0	isoniazid	Uncertain significance
katG	2156749	c.-638C>A	upstream_gene_variant	1.0	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
Rv2680	2995848	c.-257G>A	upstream_gene_variant	1.0	capreomycin
Rv2752c	3065294	c.897dupA	frameshift_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
Rv3236c	3612047	p.Ala357Val	missense_variant	1.0	pyrazinamide	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4246410	p.Tyr1060Asp	missense_variant	1.0	ethambutol
embB	4248015	p.Thr501Lys	missense_variant	0.94	ethambutol	Uncertain significance
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	4338598	c.-77G>A	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin