TB-Profiler

TB-Profiler result

Run: ERR8774253

Summary

Run ID: ERR8774253

Sample name:

Date: 2024-04-15T04:59:33.405693

Number of reads: 1672962

Percentage reads mapped: 93.47

Median coverage: 32.0

Strain: lineage2.2.2

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
lineage2	East-Asian	RD105	0.99
lineage2.2.2	East-Asian (Beijing)	RD105;RD207	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	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	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide	pncA	c.517dupG	Assoc w R
streptomycin	rrs	n.514A>C	Assoc w R
streptomycin	gid	p.Leu79Ser	Uncertain significance	Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine	alr	p.Leu113Arg		Mutation from literature
ethionamide	ethA	p.Ala381Pro	Uncertain significance	Mutation from literature
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	1472359	n.514A>C	non_coding_transcript_exon_variant	1.0	streptomycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288724	c.517dupG	frameshift_variant	1.0	pyrazinamide	Assoc w R
alr	3841083	p.Leu113Arg	missense_variant	1.0	cycloserine		Mutation from literature
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	Assoc w R
ethA	4326333	p.Ala381Pro	missense_variant	0.97	ethionamide	Uncertain significance	Mutation from literature
gid	4407967	p.Leu79Ser	missense_variant	1.0	streptomycin	Uncertain significance	Mutation from literature

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	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Not assoc w R - Interim
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
Rv0565c	657142	p.Arg110His	missense_variant	1.0	ethionamide	Uncertain significance
rpoB	763031	c.3225T>C	synonymous_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
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1254562	c.-28T>C	upstream_gene_variant	1.0	moxifloxacin	Not assoc w R
					levofloxacin	Not assoc w R
					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	1834177	c.636A>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
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	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
Rv1979c	2221939	p.Arg409Gln	missense_variant	1.0	clofazimine	Uncertain significance
Rv1979c	2221939	p.Arg409Gln	missense_variant	1.0	bedaquiline	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
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3236c	3612813	p.Thr102Ala	missense_variant	1.0	pyrazinamide	Not assoc w R - Interim
mtrB	3625065	p.Met517Leu	missense_variant	0.93	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	0.93	rifampicin	Not assoc w R
glpK	4139947	c.-192C>A	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					rifampicin
					isoniazid
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4243460	c.228C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
aftB	4267647	p.Asp397Gly	missense_variant	1.0	ethambutol	Not assoc w R
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
whiB6	4338794	c.-273A>G	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R