TB-Profiler

TB-Profiler result

Run: ERR040135

Summary

Run ID: ERR040135

Sample name:

Date: 2024-10-04T05:02:30.539713

Number of reads: 17351451

Percentage reads mapped: 99.25

Median coverage: 288.0

Strain: lineage4.6.1.2

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.6	Euro-American	None	1.0
lineage4.6.1.2	Euro-American	RD724	1.0
lineage4	Euro-American	None	1.0
lineage4.6.1	Euro-American (Uganda)	RD724	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.Ser315Asn	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Val	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.Ser315Asn	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
embB	4247429	p.Met306Val	missense_variant	0.99	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
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	7539	p.Thr80Ala	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7539	p.Thr80Ala	missense_variant	1.0	moxifloxacin	Not assoc w R - Interim
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	9276	c.1975C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrA	9276	c.1975C>T	synonymous_variant	1.0	moxifloxacin
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
rpoC	764810	p.Pro481Thr	missense_variant	1.0	rifampicin	Uncertain significance
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
fbiC	1303391	p.Arg154His	missense_variant	1.0	pretomanid
					delamanid
					clofazimine
embR	1416410	p.Leu313Arg	missense_variant	0.99	ethambutol	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	0.99	kanamycin
					capreomycin
					streptomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	0.99	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	2784617	c.-575T>C	upstream_gene_variant	1.0	kanamycin
					levofloxacin
					moxifloxacin
					streptomycin
					rifampicin
					ethambutol
					amikacin
Rv2681	2996876	c.138A>C	synonymous_variant	1.0	capreomycin	Not assoc w R
Rv2752c	3065920	p.Pro91Leu	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
whiB7	3569029	c.-350A>G	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
glpK	4139670	p.Cys29Tyr	missense_variant	0.78	levofloxacin	Not assoc w R
					moxifloxacin	Uncertain significance
					isoniazid	Uncertain significance
					streptomycin	Uncertain significance
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4245055	p.Thr608Asn	missense_variant	0.99	ethambutol	Uncertain significance
ubiA	4269131	p.Leu235Val	missense_variant	1.0	ethambutol
ethA	4327107	p.His123Tyr	missense_variant	1.0	ethionamide
ethR	4328171	p.Val208Ala	missense_variant	1.0	ethionamide
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