TB-Profiler

TB-Profiler result

Run: ERR038738

Summary

Run ID: ERR038738

Sample name:

Date: 2024-04-15T18:14:20.926921

Number of reads: 21925959

Percentage reads mapped: 99.58

Median coverage: 361.0

Strain: lineage4.6.1.1

Spoligotype:

Drug-resistance: RR-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	Euro-American	None	1.0
lineage4.6.1.1	Euro-American	RD724	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	c.1312_1314delAAC	Assoc w R - Interim
rifampicin	rpoB	c.1312_1314delAAC		Mutation from literature
p.Ser450Leu	Assoc w R
isoniazid
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide
streptomycin	gid	c.115delC	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	761114	c.1312_1314delAAC	conservative_inframe_deletion	0.62	rifampicin	Assoc w R - Interim
rpoB	761114	c.1312_1314delAAC	conservative_inframe_deletion	0.62	rifampicin		Mutation from literature
rpoB	761155	p.Ser450Leu	missense_variant	0.39	rifampicin	Assoc w R
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	Assoc w R
gid	4408087	c.115delC	frameshift_variant	0.62	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	697	p.Arg233Trp	missense_variant	1.0	isoniazid	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	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	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
hadA	732265	c.336G>A	synonymous_variant	1.0	isoniazid	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
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1253754	p.Thr261Pro	missense_variant	1.0	moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					rifampicin	Uncertain significance
					isoniazid	Uncertain significance
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
katG	2155295	p.Gly273Cys	missense_variant	0.91	isoniazid	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
Rv2477c	2784617	c.-575T>C	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin
					amikacin
Rv2681	2996876	c.138A>C	synonymous_variant	1.0	capreomycin	Not assoc w R
whiB7	3569029	c.-350A>G	upstream_gene_variant	1.0	streptomycin	Uncertain significance
					amikacin	Uncertain significance
					kanamycin	Not assoc w R
glpK	4139670	p.Cys29Tyr	missense_variant	1.0	ethambutol	Uncertain significance
					moxifloxacin	Uncertain significance
					streptomycin	Uncertain significance
					levofloxacin	Not assoc w R
					rifampicin	Uncertain significance
					isoniazid	Uncertain significance
glpK	4139859	c.-104C>T	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					rifampicin
					isoniazid
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ethA	4328329	c.-856C>G	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
gid	4407928	p.Glu92Gly	missense_variant	0.17	streptomycin	Uncertain significance