TB-Profiler

TB-Profiler result

Run: ERR552534

Summary

Run ID: ERR552534

Sample name:

Date: 2024-04-15T11:51:32.593263

Number of reads: 1646592

Percentage reads mapped: 99.6

Median coverage: 90.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	1.0
lineage4.1.2	Euro-American	None	1.0
lineage4.1.2.1	Euro-American (Haarlem)	RD182	1.0
lineage4	Euro-American	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	rpoB	p.Asp435Tyr	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide	pncA	p.Lys96Glu	Assoc w R
streptomycin	rrs	n.514A>T	Uncertain significance	Mutation from literature
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	761109	p.Asp435Tyr	missense_variant	1.0	rifampicin	Assoc w R
rrs	1472359	n.514A>T	non_coding_transcript_exon_variant	1.0	streptomycin	Uncertain significance	Mutation from literature
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288956	p.Lys96Glu	missense_variant	1.0	pyrazinamide	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
Rv0010c	13641	c.-83A>T	upstream_gene_variant	1.0	isoniazid	Uncertain significance
fgd1	491591	p.Lys270Met	missense_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Uncertain significance
mshA	575679	p.Asn111Ser	missense_variant	1.0	ethionamide	Not assoc w R
mshA	575679	p.Asn111Ser	missense_variant	1.0	isoniazid	Not assoc w R
Rv0565c	657269	p.Ser68Pro	missense_variant	1.0	ethionamide	Uncertain significance
hadA	732110	p.Cys61Gly	missense_variant	1.0	isoniazid	Uncertain significance
rpoB	760106	c.300G>A	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoB	760115	c.309C>T	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
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	781276	c.-284A>C	upstream_gene_variant	1.0	streptomycin
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1254583	c.-49A>C	upstream_gene_variant	1.0	moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rpsA	1833674	p.Lys45Glu	missense_variant	1.0	pyrazinamide	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
katG	2155241	p.Ala291Thr	missense_variant	1.0	isoniazid
PPE35	2168522	c.2091T>C	synonymous_variant	0.99	pyrazinamide
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
kasA	2518076	c.-39C>T	upstream_gene_variant	1.0	isoniazid
Rv2477c	2782415	p.Asp543Ala	missense_variant	1.0	ethambutol	Uncertain significance
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin	Uncertain significance
					amikacin
Rv2680	2996034	c.-71G>A	upstream_gene_variant	0.26	capreomycin	Uncertain significance
Rv2680	2996136	p.Ser11Asn	missense_variant	0.14	capreomycin
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
embC	4239298	c.-565C>T	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embC	4242803	p.Val981Leu	missense_variant	1.0	ethambutol	Not assoc w R
embB	4247738	p.Ala409Pro	missense_variant	1.0	ethambutol	Uncertain significance
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