TB-Profiler

TB-Profiler result

Run: SRR13837603

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: SRR13837603

Sample name:

Date: 2024-10-03T20:34:30.982533

Number of reads: 293802

Percentage reads mapped: 95.0

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
dnaA	377	p.Thr126Asn	missense_variant	1.0	isoniazid
gyrB	5709	p.Gly157Val	missense_variant	1.0	levofloxacin
gyrB	5709	p.Gly157Val	missense_variant	1.0	moxifloxacin
gyrA	9028	p.Val576Ala	missense_variant	1.0	levofloxacin
gyrA	9028	p.Val576Ala	missense_variant	1.0	moxifloxacin
mmaA3	737654	p.Ala166Ser	missense_variant	1.0	isoniazid
fbiC	1304640	c.1710A>C	synonymous_variant	1.0	pretomanid
					delamanid
					clofazimine
Rv1258c	1406376	p.Gly322Val	missense_variant	1.0	streptomycin
					pyrazinamide
					isoniazid
eis	2714940	c.392delA	frameshift_variant	1.0	kanamycin	Uncertain significance
eis	2714940	c.392delA	frameshift_variant	1.0	amikacin	Uncertain significance
fbiB	3642465	p.Asp311His	missense_variant	1.0	pretomanid
					delamanid
					clofazimine
rpoA	3878288	p.Thr74Pro	missense_variant	1.0	rifampicin
clpC1	4040792	c.-88A>T	upstream_gene_variant	1.0	pyrazinamide