TB-Profiler

TB-Profiler result

Run: ERR4819691

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: ERR4819691

Sample name:

Date: 2024-04-15T09:24:23.598776

Number of reads: 401331

Percentage reads mapped: 98.99

Median coverage: 7.0

Strain: La1.2.BCG

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
La1.2.BCG	M.bovis	None	1.0
La1.2	M.bovis	None	1.0
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
gyrA	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	moxifloxacin	Not assoc w R
Rv0565c	657578	c.-108T>C	upstream_gene_variant	1.0	ethionamide
sigE	1364961	c.549A>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
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
ndh	2103173	c.-132delG	upstream_gene_variant	1.0	ethionamide
					delamanid
					isoniazid
katG	2156465	c.-354C>T	upstream_gene_variant	1.0	isoniazid	Not assoc w R - Interim
Rv2681	2997325	p.Ala196Val	missense_variant	1.0	capreomycin	Uncertain significance
Rv3083	3448783	p.Val94Ile	missense_variant	1.0	ethionamide	Uncertain significance
lpqB	3623730	p.Ser394Leu	missense_variant	1.0	bedaquiline	Uncertain significance
lpqB	3623730	p.Ser394Leu	missense_variant	1.0	rifampicin	Not assoc w R
lpqB	3624350	c.561G>T	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
lpqB	3624350	c.561G>T	synonymous_variant	1.0	rifampicin	Not assoc w R
lpqB	3624593	c.318G>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
lpqB	3624593	c.318G>A	synonymous_variant	1.0	rifampicin	Not assoc w R
lpqB	3624710	c.201G>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
lpqB	3624710	c.201G>A	synonymous_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
clpC1	4038403	c.2302T>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
glpK	4138377	p.Val460Ala	missense_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
embC	4240671	p.Thr270Ile	missense_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4244220	c.988C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4246551	p.Asn13Ser	missense_variant	1.0	ethambutol	Not assoc w R
embB	4247173	c.660G>A	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim