TB-Profiler

TB-Profiler result

Run: ERR2653025

Summary

Run ID: ERR2653025

Sample name:

Date: 2024-10-03T15:20:26.511509

Number of reads: 1274672

Percentage reads mapped: 99.65

Median coverage: 40.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
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	kanamycin
					capreomycin
					streptomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv1979c	2222036	c.1129C>T	synonymous_variant	1.0	bedaquiline
Rv1979c	2222036	c.1129C>T	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
Rv2477c	2783811	p.Pro78Ala	missense_variant	1.0	kanamycin	Uncertain significance
					levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					streptomycin
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
					amikacin	Uncertain significance
whiB6	4338391	p.Thr44Ile	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	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