TB-Profiler

TB-Profiler result

Run: SRR4034749

Summary

Run ID: SRR4034749

Sample name:

Date: 2024-04-16T11:09:16.848396

Number of reads: 10592497

Percentage reads mapped: 99.33

Median coverage: 170.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.4.1	Euro-American (S-type)	None	1.0
lineage4	Euro-American	None	1.0
lineage4.4.1.1	Euro-American	None	0.99
lineage4.4	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.His445Asp	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide	pncA	p.Thr160Arg	Uncertain significance	Mutation from literature
streptomycin	gid	c.475delA	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	761139	p.His445Asp	missense_variant	0.99	rifampicin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288763	p.Thr160Arg	missense_variant	1.0	pyrazinamide	Uncertain significance	Mutation from literature
embB	4247431	p.Met306Ile	missense_variant	0.99	ethambutol	Assoc w R
gid	4407727	c.475delA	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
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
ndh	2102990	p.Val18Ala	missense_variant	1.0	ethionamide	Uncertain significance
					delamanid	Uncertain significance
					isoniazid	Not assoc w R
PPE35	2169840	p.Gly258Asp	missense_variant	1.0	pyrazinamide	Not assoc w R
Rv1979c	2222341	p.Met275Thr	missense_variant	1.0	clofazimine	Uncertain significance
Rv1979c	2222341	p.Met275Thr	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
Rv3083	3448608	c.105G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
Rv3236c	3612665	p.Val151Ala	missense_variant	1.0	pyrazinamide	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
fbiA	3641010	c.468C>T	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
					pretomanid
					delamanid	Not assoc w R - Interim
clpC1	4040711	c.-7G>T	upstream_gene_variant	0.99	pyrazinamide	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	4245512	c.2280G>C	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
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	4338783	c.-262C>T	upstream_gene_variant	0.99	capreomycin
					amikacin
					kanamycin