TB-Profiler

TB-Profiler result

Run: ERR11081605

Summary

Run ID: ERR11081605

Sample name:

Date: 2024-10-05T01:15:34.032661

Number of reads: 16999297

Percentage reads mapped: 99.51

Median coverage: 500.0

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.Ser450Leu	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
isoniazid	ahpC	c.-81C>T	Uncertain significance	Mutation from literature
ethambutol
pyrazinamide
streptomycin	gid	c.102delG	Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	ethA	c.1299_1300dupGT	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
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
ahpC	2726112	c.-81C>T	upstream_gene_variant	1.0	isoniazid	Uncertain significance	Mutation from literature
ethA	4326173	c.1299_1300dupGT	frameshift_variant	1.0	ethionamide	Assoc w R
gid	4408100	c.102delG	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
Rv0010c	13458	p.Thr34Met	missense_variant	1.0	isoniazid	Uncertain significance
fgd1	491591	p.Lys270Met	missense_variant	1.0	pretomanid
					delamanid	Uncertain significance
					clofazimine	Not assoc w R
mshA	575679	p.Asn111Ser	missense_variant	1.0	isoniazid	Not assoc w R
mshA	575679	p.Asn111Ser	missense_variant	1.0	ethionamide	Not assoc w R
Rv0565c	657269	p.Ser68Pro	missense_variant	1.0	ethionamide	Uncertain significance
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	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpS5	779540	c.-635A>G	upstream_gene_variant	1.0	bedaquiline
mmpS5	779540	c.-635A>G	upstream_gene_variant	1.0	clofazimine
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1253952	p.Ala195Ser	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
Rv1258c	1407462	c.-122A>C	upstream_gene_variant	0.99	streptomycin
					pyrazinamide
					isoniazid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
tsnR	1854023	p.Ala140Thr	missense_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
PPE35	2168155	p.Thr820Ala	missense_variant	1.0	pyrazinamide	Uncertain significance
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	2518076	c.-39C>T	upstream_gene_variant	1.0	isoniazid
Rv2680	2996034	c.-71G>A	upstream_gene_variant	0.16	capreomycin	Uncertain significance
thyA	3074495	c.-24C>T	upstream_gene_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3236c	3612479	p.Pro213Leu	missense_variant	1.0	pyrazinamide	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
clpC1	4039625	p.Lys360Asn	missense_variant	1.0	pyrazinamide	Uncertain significance
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	4248441	p.Thr643Ile	missense_variant	1.0	ethambutol	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin