TB-Profiler

TB-Profiler result

Run: ERR4812567

Summary

Run ID: ERR4812567

Sample name:

Date: 2024-04-15T04:35:02.908960

Number of reads: 2038559

Percentage reads mapped: 99.71

Median coverage: 58.0

Strain: lineage4

Spoligotype:

Drug-resistance: MDR-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

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin	rpoB	p.Ser450Leu	Assoc w R
isoniazid	inhA	c.-779G>T	Assoc w R - Interim	Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
isoniazid	katG	p.Ala713Pro	Uncertain significance	Mutation from literature
ethambutol	embB	p.Gly406Ala	Assoc w R
pyrazinamide	pncA	p.Asp63Ala	Assoc w R
streptomycin	rpsL	p.Lys88Thr	Uncertain significance	Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	inhA	c.-779G>T	Assoc w R - Interim	Alias fabG1_c.-17G>T
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	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
rpsL	781822	p.Lys88Thr	missense_variant	1.0	streptomycin	Uncertain significance	Mutation from literature
inhA	1673423	c.-779G>T	upstream_gene_variant	1.0	isoniazid	Assoc w R - Interim	Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA	1673423	c.-779G>T	upstream_gene_variant	1.0	ethionamide	Assoc w R - Interim	Alias fabG1_c.-17G>T
katG	2153975	p.Ala713Pro	missense_variant	1.0	isoniazid	Uncertain significance	Mutation from literature
pncA	2289054	p.Asp63Ala	missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247730	p.Gly406Ala	missense_variant	1.0	ethambutol	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	1182	c.1182G>A	synonymous_variant	1.0	isoniazid	Not assoc w R - Interim
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
gyrA	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_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
rpoB	761889	p.Val695Leu	missense_variant	1.0	rifampicin	Uncertain significance
rpoC	765462	p.Asn698Ser	missense_variant	1.0	rifampicin	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
rplC	801009	c.201A>G	synonymous_variant	1.0	linezolid	Not assoc w R - Interim
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv1979c	2223214	c.-50A>C	upstream_gene_variant	1.0	clofazimine	Uncertain significance
Rv1979c	2223214	c.-50A>C	upstream_gene_variant	1.0	bedaquiline	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
Rv2752c	3065517	c.675C>T	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
					moxifloxacin	Not assoc w R - Interim
					levofloxacin	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					isoniazid	Not assoc w R - Interim
Rv3083	3448439	c.-64delA	upstream_gene_variant	1.0	ethionamide
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269721	p.Ala38Val	missense_variant	1.0	ethambutol	Uncertain significance
ethA	4328317	c.-844C>T	upstream_gene_variant	1.0	ethionamide
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	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin