TB-Profiler

TB-Profiler result

Run: ERR2245278

Summary

Run ID: ERR2245278

Sample name:

Date: 2025-08-03T07:46:33.033835

Number of reads: 2742075

Percentage reads mapped: 99.51

Median coverage: 42.0

Strain: lineage3.1.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	100.0
lineage3.1.1	East-African-Indian	RD750	100.0

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
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

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
rpoB	759746	c.-61C>T	upstream_gene_variant	1.0	rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	amikacin	Uncertain significance
					capreomycin	Uncertain significance
					kanamycin	Uncertain significance
					streptomycin	Uncertain significance
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
PPE35	2170873	c.-262_-261insA	upstream_gene_variant	1.0	pyrazinamide	Uncertain significance
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
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	amikacin	Not assoc w R
					capreomycin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	amikacin	Uncertain significance
					capreomycin	Uncertain significance
					kanamycin	Uncertain significance
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R