TB-Profiler

TB-Profiler result

Run: ERR2517618

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: ERR2517618

Sample name:

Date: 2024-04-16T12:14:42.419661

Number of reads: 512055

Percentage reads mapped: 99.03

Median coverage: 13.0

Strain: lineage4.2.2.2

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.2.2	Euro-American (Ural)	None	0.98
lineage4.2	Euro-American	None	1.0
lineage4	Euro-American	None	1.0
lineage4.2.2.2	Euro-American (Ural)	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
isoniazid
ethambutol
pyrazinamide
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

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	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
fgd1	490787	p.Ala2Val	missense_variant	1.0	clofazimine	Uncertain significance
					pretomanid
					delamanid	Uncertain significance
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
Rv0565c	657425	p.Gly16Ser	missense_variant	1.0	ethionamide	Uncertain significance
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	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
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
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
ald	3086742	c.-78A>C	upstream_gene_variant	1.0	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin