TB-Profiler

TB-Profiler result

Run: ERR7911147

Summary

Run ID: ERR7911147

Sample name:

Date: 2024-10-05T08:47:41.834869

Number of reads: 4544394

Percentage reads mapped: 99.6

Median coverage: 152.0

Strain: lineage4.4.2

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.4	Euro-American	None	1.0
lineage4.4.2	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.Met306Val	Assoc w R
pyrazinamide	pncA	c.305delCinsGA	Assoc w R
streptomycin	rpsL	p.Lys43Arg	Assoc w R
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
rpsL	781687	p.Lys43Arg	missense_variant	1.0	streptomycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288937	c.305delCinsGA	frameshift_variant&missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247429	p.Met306Val	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
gyrA	7278	c.-24C>T	upstream_gene_variant	1.0	levofloxacin
gyrA	7278	c.-24C>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
mshA	576108	p.Ala254Gly	missense_variant	0.24	isoniazid
mshA	576108	p.Ala254Gly	missense_variant	0.24	ethionamide
nusG	734280	c.27C>T	synonymous_variant	1.0	rifampicin
mmaA3	737671	p.Ala160Val	missense_variant	1.0	isoniazid
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
rrl	1476253	n.2596A>G	non_coding_transcript_exon_variant	1.0	capreomycin
rrl	1476253	n.2596A>G	non_coding_transcript_exon_variant	1.0	linezolid
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tsnR	1854321	p.Ser239Thr	missense_variant	1.0	linezolid	Uncertain significance
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2167750	p.Asn955His	missense_variant	0.99	pyrazinamide
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
Rv2752c	3066099	p.Met31Ile	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Not assoc w R - Interim
					rifampicin	Not assoc w R
					ethambutol	Not assoc w R
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
embC	4238963	c.-900C>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
embA	4246508	c.3276G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4268928	c.906C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269089	p.Ala249Ser	missense_variant	1.0	ethambutol	Uncertain significance
ubiA	4269375	c.459G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
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