TB-Profiler

TB-Profiler result

Run: ERR13266033

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: ERR13266033

Sample name:

Date: 2025-02-11T09:59:33.320787

Number of reads: 305787

Percentage reads mapped: 99.47

Median coverage: 7.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON

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

Lineage	Family	RDs	Frequency
lineage4.2	Euro-American	None	0.61
lineage4	Euro-American	None	1.0
lineage4.2.1	Euro-American (TUR)	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	embB	p.Met306Ile	Assoc w R
ethambutol	embB	p.Asp1024Asn	Uncertain significance	Mutation from literature
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid	rplC	p.Cys154Arg	Assoc w R

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
rplC	801268	p.Cys154Arg	missense_variant	1.0	linezolid	Assoc w R
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	Assoc w R
embB	4249583	p.Asp1024Asn	missense_variant	1.0	ethambutol	Uncertain significance	Mutation from literature

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	1471587	n.-259A>C	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
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
ald	3086742	c.-78A>C	upstream_gene_variant	1.0	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embB	4249594	c.3081G>A	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin