TB-Profiler

TB-Profiler result

Run: ERR2693264

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: ERR2693264

Sample name:

Date: 2024-04-15T23:48:22.681091

Number of reads: 288556

Percentage reads mapped: 94.44

Median coverage: 8.0

Strain: La1.8.1

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON

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

Lineage	Family	RDs	Frequency
La1.8	M.bovis	None	1.0
La1.8.1	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
rifampicin
isoniazid
ethambutol
pyrazinamide	pncA	p.His57Asp	Assoc w R
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
pncA	2289073	p.His57Asp	missense_variant	1.0	pyrazinamide	Assoc w R

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
gyrB	6406	c.1167C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrB	6406	c.1167C>T	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
gyrB	6446	p.Ala403Ser	missense_variant	1.0	levofloxacin	Not assoc w R
gyrB	6446	p.Ala403Ser	missense_variant	1.0	moxifloxacin	Uncertain significance
gyrA	8048	c.747C>A	synonymous_variant	1.0	levofloxacin
gyrA	8048	c.747C>A	synonymous_variant	1.0	moxifloxacin
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
rplC	801454	p.Glu216Gln	missense_variant	1.0	linezolid
inhA	1673715	c.-487C>G	upstream_gene_variant	1.0	ethionamide	Uncertain significance
inhA	1673715	c.-487C>G	upstream_gene_variant	1.0	isoniazid	Uncertain significance
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
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	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
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
embB	4248734	p.Arg741Trp	missense_variant	1.0	ethambutol	Uncertain significance
ubiA	4269387	p.Glu149Asp	missense_variant	1.0	ethambutol	Not assoc w R
ethA	4326024	p.Pro484Ser	missense_variant	1.0	ethionamide