TB-Profiler

TB-Profiler result

Run: ERR7737755

Summary

Run ID: ERR7737755

Sample name:

Date: 2024-04-16T12:51:37.169618

Number of reads: 3286801

Percentage reads mapped: 99.68

Median coverage: 91.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: RR-TB

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

Lineage	Family	RDs	Frequency
lineage4.7	Euro-American (mainly T)	None	1.0
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
rifampicin	rpoB	p.Leu430Pro	Assoc w R
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
rpoB	761095	p.Leu430Pro	missense_variant	1.0	rifampicin	Assoc w R

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
dnaA	1126	c.1126C>T	synonymous_variant	1.0	isoniazid	Not assoc w R - Interim
gyrB	7139	p.Arg634Cys	missense_variant	0.92	levofloxacin
gyrB	7139	p.Arg634Cys	missense_variant	0.92	moxifloxacin
gyrA	7362	p.Glu21Gln	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
fgd1	490779	c.-4A>G	upstream_gene_variant	0.99	clofazimine	Uncertain significance
					pretomanid
					delamanid	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	775639	p.Ile948Val	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
Rv1258c	1407604	c.-264C>T	upstream_gene_variant	1.0	streptomycin
					isoniazid
					pyrazinamide
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrl	1474294	n.637C>G	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1474294	n.637C>G	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2170675	c.-63G>C	upstream_gene_variant	1.0	pyrazinamide	Uncertain significance
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
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4249732	c.3219C>G	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