TB-Profiler

TB-Profiler result

Run: SRR13861252

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: SRR13861252

Sample name:

Date: 2024-10-04T23:33:18.221460

Number of reads: 235460

Percentage reads mapped: 11.78

Median coverage: 8.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON

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
mmpR5	778439	c.-551C>A	upstream_gene_variant	1.0	bedaquiline
mmpR5	778439	c.-551C>A	upstream_gene_variant	1.0	clofazimine
rplC	801357	p.His183Gln	missense_variant	1.0	linezolid
ndh	2102525	p.Phe173Tyr	missense_variant	1.0	isoniazid
					delamanid
					ethionamide
ndh	2102538	c.504_505insT	frameshift_variant	1.0	isoniazid	Uncertain significance
					delamanid	Uncertain significance
					ethionamide	Uncertain significance
pncA	2289415	c.-174C>G	upstream_gene_variant	1.0	pyrazinamide
eis	2714983	p.Ala117Glu	missense_variant	1.0	kanamycin
eis	2714983	p.Ala117Glu	missense_variant	1.0	amikacin
fbiB	3642056	c.522C>G	synonymous_variant	1.0	pretomanid
					delamanid
					clofazimine
rpoA	3877967	p.Thr181Ser	missense_variant	1.0	rifampicin	Uncertain significance
rpoA	3877972	c.535delG	frameshift_variant	1.0	rifampicin