TB-Profiler

TB-Profiler result

Run: ERR2245351

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: ERR2245351

Sample name:

Date: 2024-04-14T23:26:02.513352

Number of reads: 1603399

Percentage reads mapped: 99.26

Median coverage: 26.0

Strain: lineage3.1.1;lineage4

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	1.0
lineage3.1.1	East-African-Indian	RD750	0.53
lineage4	Euro-American	None	0.67

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
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embC	4242075	p.Arg738Gln	missense_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R