TB-Profiler

TB-Profiler result

Run: SRR13837674

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: SRR13837674

Sample name:

Date: 2024-04-16T05:49:36.227746

Number of reads: 293828

Percentage reads mapped: 96.0

Median coverage: 10.0

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
rpoB	762083	c.2277T>A	synonymous_variant	1.0	rifampicin
rpoC	766578	p.Asp1070Val	missense_variant	1.0	rifampicin
mmpL5	776436	p.Ala682Gly	missense_variant	1.0	clofazimine
mmpL5	776436	p.Ala682Gly	missense_variant	1.0	bedaquiline
pncA	2290201	c.-960G>A	upstream_gene_variant	1.0	pyrazinamide
kasA	2518058	c.-57G>A	upstream_gene_variant	1.0	isoniazid
eis	2714947	p.Phe129Ser	missense_variant	1.0	amikacin
eis	2714947	p.Phe129Ser	missense_variant	1.0	kanamycin
whiB7	3568660	p.Pro7Leu	missense_variant	1.0	streptomycin	Uncertain significance
					amikacin
					kanamycin
mtrA	3627016	p.Leu112Val	missense_variant	1.0	bedaquiline
mtrA	3627016	p.Leu112Val	missense_variant	1.0	rifampicin
ddn	3986940	p.Asp33His	missense_variant	1.0	delamanid
ddn	3986940	p.Asp33His	missense_variant	1.0	pretomanid
glpK	4138519	p.Glu413*	stop_gained	1.0	ethambutol	Uncertain significance
					moxifloxacin	Uncertain significance
					streptomycin	Uncertain significance
					levofloxacin	Uncertain significance
					rifampicin	Uncertain significance
					isoniazid	Uncertain significance