TB-Profiler

TB-Profiler result

Run: ERR4423593

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: ERR4423593

Sample name:

Date: 2024-10-04T11:01:58.641773

Number of reads: 501179

Percentage reads mapped: 99.52

Median coverage: 9.0

Strain: lineage4.1.3

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
lineage4.1.3	Euro-American	None	1.0
lineage4.1	Euro-American	None	0.58
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
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
fbiC	1304610	c.1680C>T	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R - Interim
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
lpqB	3623291	c.1620C>A	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
lpqB	3623291	c.1620C>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embC	4242803	p.Val981Leu	missense_variant	1.0	ethambutol	Not assoc w R