TB-Profiler

TB-Profiler result

Run: ERR2747625

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: ERR2747625

Sample name:

Date: 2024-04-16T09:38:34.861864

Number of reads: 220105

Percentage reads mapped: 60.83

Median coverage: 3.0

Strain: La1.8.1;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
La1.8.1	M.bovis	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	0.76
La1	M.bovis	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
bacA	2062922	p.Ile603Val	missense_variant	1.0	streptomycin	Not assoc w R
					kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
Rv2681	2997325	p.Ala196Val	missense_variant	1.0	capreomycin	Uncertain significance
clpC1	4038403	c.2302T>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim