TB-Profiler

TB-Profiler result

Run: ERR11068202

Summary

Run ID: ERR11068202

Sample name:

Date: 2024-04-15T08:33:42.373516

Number of reads: 6564892

Percentage reads mapped: 99.76

Median coverage: 203.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.8	Euro-American (mainly T)	RD219	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	katG	p.Tyr155Cys	Uncertain significance	Mutation from literature
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
katG	2155648	p.Tyr155Cys	missense_variant	1.0	isoniazid	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
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
mshA	575357	p.Val4Met	missense_variant	1.0	ethionamide	Uncertain significance
mshA	575357	p.Val4Met	missense_variant	1.0	isoniazid	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
fbiC	1302684	c.-247C>T	upstream_gene_variant	1.0	clofazimine
					pretomanid
					delamanid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1474001	n.344C>T	non_coding_transcript_exon_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
bacA	2064078	c.651G>A	synonymous_variant	1.0	streptomycin	Not assoc w R - Interim
					kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R - Interim
					amikacin	Not assoc w R - Interim
PPE35	2168149	p.Pro822Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
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
Rv2680	2995848	c.-257G>A	upstream_gene_variant	1.0	capreomycin
Rv3083	3448507	c.5_*1408del	frameshift_variant&stop_lost&splice_region_variant	1.0	ethionamide	Uncertain significance
embC	4242643	c.2781C>T	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