TB-Profiler

TB-Profiler result

Run: ERR4797026

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: ERR4797026

Sample name:

Date: 2024-04-15T11:36:17.919053

Number of reads: 287469

Percentage reads mapped: 99.26

Median coverage: 8.0

Strain: lineage1.1.2

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
lineage1.1.2	Indo-Oceanic	RD239	0.5
lineage1.1	Indo-Oceanic	RD239	0.59
lineage1	Indo-Oceanic	RD239	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
gyrB	6112	p.Met291Ile	missense_variant	1.0	levofloxacin	Not assoc w R
gyrB	6112	p.Met291Ile	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrB	6124	c.885C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R
gyrB	6124	c.885C>T	synonymous_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9143	c.1842T>C	synonymous_variant	1.0	levofloxacin	Not assoc w R
gyrA	9143	c.1842T>C	synonymous_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
fgd1	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Not assoc w R - Interim
rpoC	765171	p.Pro601Leu	missense_variant	1.0	rifampicin	Not assoc w R
rpoC	767248	c.3879C>T	synonymous_variant	1.0	rifampicin
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
embR	1417793	c.-446C>T	upstream_gene_variant	1.0	ethambutol
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
katG	2154431	p.His561Tyr	missense_variant	1.0	isoniazid
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
kasA	2518132	c.18C>T	synonymous_variant	1.0	isoniazid
ahpC	2726022	c.-171C>T	upstream_gene_variant	1.0	isoniazid
ahpC	2726051	c.-142G>A	upstream_gene_variant	1.0	isoniazid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embA	4243848	p.Val206Met	missense_variant	1.0	ethambutol	Not assoc w R
embB	4247646	p.Glu378Ala	missense_variant	1.0	ethambutol	Not assoc w R
ubiA	4269606	c.228T>C	synonymous_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
whiB6	4338603	c.-82C>T	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
gid	4407873	c.330G>T	synonymous_variant	1.0	streptomycin	Not assoc w R