TB-Profiler

TB-Profiler result

Run: ERR4553573

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: ERR4553573

Sample name:

Date: 2024-10-04T23:07:18.900495

Number of reads: 885004

Percentage reads mapped: 99.57

Median coverage: 27.0

Strain: lineage1.1.3.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage1.1.3	Indo-Oceanic	RD239	1.0
lineage1.1	Indo-Oceanic	RD239	0.34
lineage1.1.3.1	Indo-Oceanic	RD239	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.Glu504Asp	Uncertain significance	Mutation from literature
pyrazinamide
streptomycin	rpsL	p.Lys43Arg	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
rpsL	781687	p.Lys43Arg	missense_variant	1.0	streptomycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
embB	4248025	p.Glu504Asp	missense_variant	1.0	ethambutol	Uncertain significance	Mutation from literature

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
gyrB	7051	c.1812A>G	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrB	7051	c.1812A>G	synonymous_variant	1.0	moxifloxacin
gyrB	7124	p.Ser629Ala	missense_variant	1.0	levofloxacin	Uncertain significance
gyrB	7124	p.Ser629Ala	missense_variant	1.0	moxifloxacin
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	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R
Rv0565c	657578	c.-108T>C	upstream_gene_variant	1.0	ethionamide
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	764363	p.Gly332Ser	missense_variant	0.89	rifampicin	Uncertain significance
rpoC	764689	c.1320G>A	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
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
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
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	levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					isoniazid	Not assoc w R
					rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1474234	n.577G>A	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1474234	n.577G>A	non_coding_transcript_exon_variant	1.0	linezolid
tsnR	1854045	p.Tyr147Cys	missense_variant	1.0	linezolid	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
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	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
kasA	2518132	c.18C>T	synonymous_variant	1.0	isoniazid
folC	2747182	c.417G>A	synonymous_variant	1.0	para-aminosalicylic_acid
ribD	2987570	c.732C>T	synonymous_variant	1.0	para-aminosalicylic_acid
Rv2752c	3066791	c.-600G>A	upstream_gene_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
					ethambutol
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
fbiD	3339521	p.His135Arg	missense_variant	1.0	pretomanid
					delamanid
					clofazimine
lpqB	3624486	p.Asp142Gly	missense_variant	1.0	rifampicin	Not assoc w R
lpqB	3624486	p.Asp142Gly	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
alr	3841253	c.168C>T	synonymous_variant	1.0	cycloserine
glpK	4138377	p.Val460Ala	missense_variant	1.0	levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					isoniazid	Not assoc w R
					streptomycin	Not assoc w R
					rifampicin	Not assoc w R
					ethambutol	Not assoc w R
embC	4240671	p.Thr270Ile	missense_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4243848	p.Val206Met	missense_variant	1.0	ethambutol	Not assoc w R
whiB6	4338429	c.-218_92del	frameshift_variant&start_lost	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407780	c.423G>A	synonymous_variant	1.0	streptomycin	Not assoc w R - Interim