TB-Profiler

TB-Profiler result

Run: ERR2707186

Summary

Run ID: ERR2707186

Sample name:

Date: 2024-03-26T22:34:25.933429

Number of reads: 3184079

Percentage reads mapped: 99.75

Median coverage: 99.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: MDR-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
lineage4.9	Euro-American (H37Rv-like)	None	1.0

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin	rpoB	p.His445Asp	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide
streptomycin	rpsL	p.Lys88Arg	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	761139	p.His445Asp	missense_variant	1.0	rifampicin	Assoc w R
rpsL	781822	p.Lys88Arg	missense_variant	1.0	streptomycin	Assoc w R
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
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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2168738	p.Phe625Leu	missense_variant	1.0	pyrazinamide
whiB6	4338195	p.His109Gln	missense_variant	1.0	capreomycin	Uncertain significance
					amikacin
					kanamycin	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338599	c.-78A>C	upstream_gene_variant	1.0	capreomycin
					amikacin	Uncertain significance
					kanamycin