TB-Profiler

TB-Profiler result

Run: ERR2653077

Summary

Run ID: ERR2653077

Sample name:

Date: 2024-10-04T06:57:21.208293

Number of reads: 18721545

Percentage reads mapped: 98.52

Median coverage: 514.0

Strain: lineage4.3.4.2

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.3	Euro-American (LAM)	None	1.0
lineage4	Euro-American	None	1.0
lineage4.3.4	Euro-American (LAM)	RD174	1.0
lineage4.3.4.2	Euro-American (LAM)	RD174	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	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide	pncA	p.Thr76Pro	Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	ethA	c.1394dupT	Assoc w R
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	0.99	rifampicin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2289016	p.Thr76Pro	missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	Assoc w R
ethA	4326079	c.1394dupT	frameshift_variant	1.0	ethionamide	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
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	761032	p.Gln409Arg	missense_variant	1.0	rifampicin	Uncertain significance
rpoC	764995	c.1626C>G	synonymous_variant	1.0	rifampicin	Not assoc w R
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
embR	1417792	c.-445G>C	upstream_gene_variant	0.99	ethambutol
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					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	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
Rv2477c	2784613	c.-571T>C	upstream_gene_variant	1.0	kanamycin
					levofloxacin
					moxifloxacin
					streptomycin
					rifampicin
					ethambutol
					amikacin
Rv2752c	3065293	p.Val300Ala	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Not assoc w R - Interim
					rifampicin	Not assoc w R
					ethambutol	Not assoc w R
thyA	3073868	p.Thr202Ala	missense_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3236c	3612009	p.Ala370Thr	missense_variant	1.0	pyrazinamide	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3626633	c.-20G>A	upstream_gene_variant	1.0	rifampicin	Uncertain significance
mtrB	3626633	c.-20G>A	upstream_gene_variant	1.0	bedaquiline	Uncertain significance
clpC1	4038287	c.2418C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
embC	4239763	c.-100C>T	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4247884	c.1371C>A	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
embB	4248646	c.2133C>T	synonymous_variant	1.0	ethambutol
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
gid	4408016	p.Asp63His	missense_variant	0.99	streptomycin	Uncertain significance
gid	4408156	p.Leu16Arg	missense_variant	1.0	streptomycin	Not assoc w R