TB-Profiler

TB-Profiler result

Run: SRR4037743

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: SRR4037743

Sample name:

Date: 2024-10-05T03:46:00.190965

Number of reads: 438555

Percentage reads mapped: 99.66

Median coverage: 9.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.4.1	Euro-American (S-type)	None	0.99
lineage4	Euro-American	None	1.0
lineage4.4.1.1	Euro-American	None	1.0
lineage4.4	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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
ndh	2102990	p.Val18Ala	missense_variant	1.0	isoniazid	Not assoc w R
					delamanid	Uncertain significance
					ethionamide	Uncertain significance
PPE35	2168479	p.Thr712Pro	missense_variant	1.0	pyrazinamide	Not assoc w R
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3083	3448608	c.105G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
whiB7	3568779	c.-100T>C	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					amikacin	Not assoc w R
					streptomycin	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R