TB-Profiler

TB-Profiler result

Run: ERR4553429

Summary

Run ID: ERR4553429

Sample name:

Date: 2024-10-05T09:53:39.224932

Number of reads: 1828607

Percentage reads mapped: 99.54

Median coverage: 58.0

Strain:

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage1.2.2	Indo-Oceanic	RD239	1.0
lineage1.2.2.2	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
isoniazid	inhA	c.-770T>G	Assoc w R - Interim	Alias fabG1_c.-8T>G. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide	pncA	p.Val139Ala	Assoc w R
streptomycin
fluoroquinolones
moxifloxacin	gyrB	p.Thr500Asn	Uncertain significance	Mutation from literature
ofloxacin
levofloxacin	gyrB	p.Thr500Asn	Uncertain significance	Mutation from literature
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin	eis	c.-37G>T	Assoc w R
cycloserine
ethionamide	inhA	c.-770T>G	Assoc w R - Interim	Alias fabG1_c.-8T>G
ethionamide	ethA	c.197dupT	Assoc w R
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
gyrB	6738	p.Thr500Asn	missense_variant	1.0	levofloxacin	Uncertain significance	Mutation from literature
gyrB	6738	p.Thr500Asn	missense_variant	1.0	moxifloxacin	Uncertain significance	Mutation from literature
inhA	1673432	c.-770T>G	upstream_gene_variant	1.0	ethionamide	Assoc w R - Interim	Alias fabG1_c.-8T>G
inhA	1673432	c.-770T>G	upstream_gene_variant	1.0	isoniazid	Assoc w R - Interim	Alias fabG1_c.-8T>G. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288826	p.Val139Ala	missense_variant	1.0	pyrazinamide	Assoc w R
eis	2715369	c.-37G>T	upstream_gene_variant	1.0	kanamycin	Assoc w R
ethA	4327276	c.197dupT	frameshift_variant	1.0	ethionamide	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
gyrB	5075	c.-165C>T	upstream_gene_variant	1.0	levofloxacin
gyrB	5075	c.-165C>T	upstream_gene_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
Rv0010c	13699	c.-141A>G	upstream_gene_variant	1.0	isoniazid	Not assoc w R
fgd1	491359	p.Ile193Leu	missense_variant	1.0	pretomanid
					delamanid
					clofazimine
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	761277	p.Ile491Leu	missense_variant	1.0	rifampicin	Uncertain significance
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	767011	c.3642G>C	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	1473817	n.160T>C	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1473817	n.160T>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
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	2064486	c.243A>G	synonymous_variant	1.0	kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R - Interim
					streptomycin	Not assoc w R - Interim
					amikacin	Not assoc w R - Interim
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
katG	2156614	c.-503A>C	upstream_gene_variant	1.0	isoniazid	Uncertain significance
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
PPE35	2168742	p.Gly624Asp	missense_variant	1.0	pyrazinamide	Uncertain significance
Rv1979c	2221725	c.1440T>G	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2221725	c.1440T>G	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
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
Rv1979c	2223553	c.-389C>A	upstream_gene_variant	1.0	bedaquiline	Uncertain significance
Rv1979c	2223553	c.-389C>A	upstream_gene_variant	1.0	clofazimine	Not assoc w R
kasA	2518132	c.18C>T	synonymous_variant	1.0	isoniazid
Rv2752c	3064889	p.Lys435Glu	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					ethambutol	Uncertain significance
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3083	3448391	c.-113C>T	upstream_gene_variant	1.0	ethionamide
lpqB	3623569	c.1342C>T	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
lpqB	3623569	c.1342C>T	synonymous_variant	1.0	bedaquiline
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
mtrA	3627602	c.-253C>T	upstream_gene_variant	1.0	rifampicin	Uncertain significance
mtrA	3627602	c.-253C>T	upstream_gene_variant	1.0	bedaquiline	Uncertain significance
alr	3841546	c.-126C>A	upstream_gene_variant	1.0	cycloserine
alr	3841568	c.-148G>A	upstream_gene_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
ethA	4326439	p.Asn345Lys	missense_variant	1.0	ethionamide	Uncertain significance
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407901	p.Leu101Pro	missense_variant	1.0	streptomycin	Uncertain significance