TB-Profiler

TB-Profiler result

Run: ERR10680208

Summary

Run ID: ERR10680208

Sample name:

Date: 2024-04-14T16:00:44.547070

Number of reads: 7871924

Percentage reads mapped: 99.75

Median coverage: 229.0

Strain: lineage4.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	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	Comment
rifampicin	rpoB	p.Asp435Val	Assoc w R
isoniazid	katG	c.531_540delCTTCAAGACG	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
ethambutol	embB	p.Gly406Asp	Assoc w R
pyrazinamide	pncA	p.Thr142Met	Assoc w R
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	761110	p.Asp435Val	missense_variant	1.0	rifampicin	Assoc w R
katG	2155571	c.531_540delCTTCAAGACG	frameshift_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288817	p.Thr142Met	missense_variant	0.23	pyrazinamide	Assoc w R
embB	4247431	p.Met306Ile	missense_variant	0.57	ethambutol	Assoc w R
embB	4247730	p.Gly406Asp	missense_variant	0.23	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
gyrB	5724	p.Ala162Val	missense_variant	1.0	levofloxacin
gyrB	5724	p.Ala162Val	missense_variant	1.0	moxifloxacin
gyrB	6507	p.Ala423Val	missense_variant	1.0	levofloxacin	Uncertain significance
gyrB	6507	p.Ala423Val	missense_variant	1.0	moxifloxacin	Uncertain significance
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
gyrA	9656	c.2355C>G	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrA	9656	c.2355C>G	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
Rv0565c	657269	p.Ser68Pro	missense_variant	1.0	ethionamide	Uncertain significance
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rpoC	765187	c.1818C>T	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
rpoC	766012	c.2643C>G	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
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
mmpL5	775973	p.Leu836Phe	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	775973	p.Leu836Phe	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	776411	c.2070T>C	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
mmpL5	776411	c.2070T>C	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rpsL	781421	c.-139C>A	upstream_gene_variant	1.0	streptomycin	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rpsA	1834660	c.1119C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
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
katG	2156007	c.105C>T	synonymous_variant	0.99	isoniazid	Not assoc w R - Interim
PPE35	2170748	c.-136C>T	upstream_gene_variant	1.0	pyrazinamide
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
Rv2477c	2784617	c.-575T>C	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin
					amikacin
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrA	3627293	c.57G>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
mtrA	3627293	c.57G>A	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
rpoA	3878588	c.-81G>A	upstream_gene_variant	1.0	rifampicin	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embC	4242803	p.Val981Leu	missense_variant	1.0	ethambutol	Not assoc w R
embB	4248758	c.2245C>T	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
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