TB-Profiler

TB-Profiler result

Run: SAMN02053777

Summary

Run ID: SAMN02053777

Sample name:

Date: 2024-10-04T00:18:06.551471

Number of reads: 17531866

Percentage reads mapped: 99.1

Median coverage: 372.0

Strain: lineage4.3.2.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.3	Euro-American (LAM)	None	1.0
lineage4.3.2	Euro-American (LAM)	None	1.0
lineage4.3.2.1	Euro-American (LAM)	RD761	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
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide	pncA	p.Lys96Arg	Assoc w R
streptomycin
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
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288955	p.Lys96Arg	missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	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	5520	p.Pro94Leu	missense_variant	1.0	levofloxacin	Not assoc w R
gyrB	5520	p.Pro94Leu	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrB	7222	c.1983C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R
gyrB	7222	c.1983C>T	synonymous_variant	1.0	moxifloxacin	Not assoc w R
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
rpoB	762277	p.Arg824Leu	missense_variant	1.0	rifampicin	Uncertain significance
rpoC	764995	c.1626C>G	synonymous_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
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	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472337	n.492C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					amikacin	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
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
Rv2477c	2784613	c.-571T>C	upstream_gene_variant	1.0	kanamycin
					levofloxacin
					moxifloxacin
					streptomycin
					rifampicin
					ethambutol
					amikacin
ribD	2986827	c.-12G>A	upstream_gene_variant	1.0	para-aminosalicylic_acid
thyA	3073868	p.Thr202Ala	missense_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
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	4038287	c.2418C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4247097	p.Pro195His	missense_variant	1.0	ethambutol	Uncertain significance
ubiA	4269308	p.Phe176Leu	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
gid	4407955	p.Arg83Gln	missense_variant	1.0	streptomycin	Uncertain significance
gid	4408156	p.Leu16Arg	missense_variant	1.0	streptomycin	Not assoc w R