TB-Profiler

TB-Profiler result

Run: SRR18715122

Summary

Run ID: SRR18715122

Sample name:

Date: 2024-04-16T01:07:00.528806

Number of reads: 3397450

Percentage reads mapped: 99.51

Median coverage: 103.0

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.Asp435Val	Assoc w R
isoniazid	ahpC	c.-74G>A	Uncertain significance	Mutation from literature
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin	rrs	n.1401A>G	Assoc w R
capreomycin	rrs	n.1401A>G	Assoc w R
kanamycin	rrs	n.1401A>G	Assoc w R
cycloserine
ethionamide	ethA	c.1270delT	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	761110	p.Asp435Val	missense_variant	1.0	rifampicin	Assoc w R
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	1.0	amikacin	Assoc w R
					kanamycin	Assoc w R
					capreomycin	Assoc w R
ahpC	2726119	c.-74G>A	upstream_gene_variant	0.99	isoniazid	Uncertain significance	Mutation from literature
ethA	4326203	c.1270delT	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
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	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	732244	c.315C>T	synonymous_variant	1.0	isoniazid	Not assoc w R - Interim
rpoB	760115	c.309C>T	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoB	763244	c.3438C>T	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
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	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
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	2154491	p.Ala541Thr	missense_variant	1.0	isoniazid	Uncertain significance
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
eis	2715670	c.-338C>T	upstream_gene_variant	1.0	amikacin
eis	2715670	c.-338C>T	upstream_gene_variant	1.0	kanamycin
Rv2477c	2783635	c.405_407dupGGA	disruptive_inframe_insertion	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin
					amikacin
Rv2680	2996034	c.-71G>A	upstream_gene_variant	0.14	capreomycin	Uncertain significance
Rv2680	2996136	p.Ser11Asn	missense_variant	0.18	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
ubiA	4269743	p.Leu31Val	missense_variant	1.0	ethambutol	Uncertain significance
aftB	4269747	c.-911C>T	upstream_gene_variant	1.0	ethambutol
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