TB-Profiler

TB-Profiler result

Run: SRR1173265

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: SRR1173265

Sample name:

Date: 2024-10-04T20:46:57.273473

Number of reads: 281899

Percentage reads mapped: 97.1

Median coverage: 6.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	0.52
lineage4.1.2	Euro-American	None	1.0
lineage4	Euro-American	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
Rv0565c	656832	c.639G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
rpoB	760115	c.309C>T	synonymous_variant	1.0	rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
PPE35	2168501	p.Phe704Leu	missense_variant	1.0	pyrazinamide	Uncertain significance