TB-Profiler

TB-Profiler result

Run: ERR4423686

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: ERR4423686

Sample name:

Date: 2024-04-15T23:57:41.703526

Number of reads: 1098247

Percentage reads mapped: 99.56

Median coverage: 19.0

Strain: lineage3.1.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	1.0
lineage3.1.1	East-African-Indian	RD750	1.0
lineage3.1	East-African-Indian	RD750	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.Gly406Ala	Assoc w R
pyrazinamide	pncA	c.-448_*4192del	Assoc w R
streptomycin	gid	c.351delG	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	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2284488	c.-448_*4192del	transcript_ablation	1.0	pyrazinamide	Assoc w R
embB	4247730	p.Gly406Ala	missense_variant	1.0	ethambutol	Assoc w R
gid	4407851	c.351delG	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	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	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Not assoc w R - Interim
rpoB	759746	c.-61C>T	upstream_gene_variant	1.0	rifampicin	Not assoc w R
rpoB	762434	c.2628T>G	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	767123	p.Val1252Met	missense_variant	1.0	rifampicin	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
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776100	p.Thr794Ile	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	1254562	c.-28T>C	upstream_gene_variant	1.0	moxifloxacin	Not assoc w R
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
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
PPE35	2170461	p.Gly51Glu	missense_variant	1.0	pyrazinamide	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
ahpC	2726105	c.-88G>A	upstream_gene_variant	1.0	isoniazid	Not assoc w R
Rv2477c	2782498	c.1545C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					levofloxacin	Not assoc w R
					kanamycin	Not assoc w R
					rifampicin	Not assoc w R
					amikacin	Not assoc w R
Rv2477c	2783814	p.Pro77Ser	missense_variant	1.0	ethambutol	Uncertain significance
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin	Uncertain significance
					amikacin
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
panD	4044872	c.-591C>T	upstream_gene_variant	1.0	pyrazinamide
glpK	4138622	c.1134C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
embC	4240172	p.Val104Met	missense_variant	1.0	ethambutol	Not assoc w R
embC	4241562	p.Arg567His	missense_variant	1.0	ethambutol	Not assoc w R
embC	4242075	p.Arg738Gln	missense_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269311	p.Trp175Gly	missense_variant	1.0	ethambutol	Uncertain significance
whiB6	4338594	c.-73T>G	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
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	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R