TB-Profiler

TB-Profiler result

Run: ERR8773556

Summary

Run ID: ERR8773556

Sample name:

Date: 2024-04-15T07:16:25.486716

Number of reads: 2117423

Percentage reads mapped: 99.5

Median coverage: 45.0

Strain: lineage4.2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.2.2.1	Euro-American	None	1.0
lineage4.2.2	Euro-American (Ural)	None	1.0
lineage4.2	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.His445Asp	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide
streptomycin	gid	c.102delG	Assoc w R
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	761139	p.His445Asp	missense_variant	1.0	rifampicin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	Assoc w R
gid	4408100	c.102delG	frameshift_variant	1.0	streptomycin	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	1131	c.1131C>A	synonymous_variant	0.98	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	0.98	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	0.98	moxifloxacin	Not assoc w R
gyrA	7709	c.408G>A	synonymous_variant	1.0	levofloxacin
gyrA	7709	c.408G>A	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
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
Rv0010c	13876	c.-318G>C	upstream_gene_variant	1.0	isoniazid
mshA	576077	c.730C>T	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
mshA	576077	c.730C>T	synonymous_variant	1.0	isoniazid	Not assoc w R
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	800204	c.-605T>C	upstream_gene_variant	1.0	linezolid
rrs	1471659	n.-187C>T	upstream_gene_variant	0.98	streptomycin
					kanamycin
					capreomycin
					amikacin
fabG1	1673327	c.-113A>C	upstream_gene_variant	1.0	ethionamide
fabG1	1673327	c.-113A>C	upstream_gene_variant	1.0	isoniazid
rpsA	1834823	p.His428Tyr	missense_variant	1.0	pyrazinamide
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917908	c.-32C>G	upstream_gene_variant	1.0	capreomycin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
bacA	2063685	c.1044G>A	synonymous_variant	1.0	streptomycin	Not assoc w R - Interim
					kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
bacA	2063911	p.Ile273Thr	missense_variant	1.0	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
PPE35	2169952	p.Asn221Asp	missense_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
Rv2752c	3066280	c.-89C>T	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					levofloxacin
					rifampicin
					isoniazid
thyA	3074495	c.-24C>T	upstream_gene_variant	0.98	para-aminosalicylic_acid
ald	3086742	c.-78A>C	upstream_gene_variant	1.0	cycloserine
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
embC	4239334	c.-529T>C	upstream_gene_variant	1.0	ethambutol	Not assoc w R
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
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin