TB-Profiler

TB-Profiler result

Run: SRR28393623

Summary

Run ID: SRR28393623

Sample name:

Date: 2024-05-22T08:25:32.066655

Number of reads: 3770434

Percentage reads mapped: 99.82

Median coverage: 107.0

Strain: lineage4.3.4.2

Spoligotype:

Drug-resistance: Pre-XDR-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	Euro-American	None	1.0
lineage4.3.4	Euro-American (LAM)	RD174	1.0
lineage4.3.4.2	Euro-American (LAM)	RD174	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.Asp328Tyr	Assoc w R
pyrazinamide	pncA	p.Ala146Val	Assoc w R
streptomycin
fluoroquinolones
moxifloxacin	gyrA	p.Asp94Ala	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin	gyrA	p.Asp94Ala	Assoc w R
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
gyrA	7582	p.Asp94Ala	missense_variant	0.99	moxifloxacin	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA	7582	p.Asp94Ala	missense_variant	0.99	levofloxacin	Assoc w R
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	2288805	p.Ala146Val	missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247495	p.Asp328Tyr	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	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
rpoC	764817	p.Val483Gly	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	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
Rv1129c	1254588	c.-54T>G	upstream_gene_variant	1.0	moxifloxacin
					levofloxacin
					rifampicin
					isoniazid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
inhA	1673406	c.-796C>T	upstream_gene_variant	0.78	ethionamide	Uncertain significance
inhA	1673406	c.-796C>T	upstream_gene_variant	0.78	isoniazid	Uncertain significance
rpsA	1834505	p.His322Tyr	missense_variant	1.0	pyrazinamide	Uncertain significance
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	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
folC	2747453	p.Arg49Gln	missense_variant	0.98	para-aminosalicylic_acid
Rv2477c	2783962	c.81T>C	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
					moxifloxacin	Not assoc w R - Interim
					streptomycin	Not assoc w R - Interim
					levofloxacin
					kanamycin	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					amikacin	Not assoc w R - Interim
Rv2477c	2784613	c.-571T>C	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin
					amikacin
thyA	3073868	p.Thr202Ala	missense_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3236c	3612009	p.Ala370Thr	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
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
embA	4243190	c.-43G>C	upstream_gene_variant	0.99	ethambutol	Uncertain significance
embA	4243590	p.Asp120Asn	missense_variant	1.0	ethambutol	Uncertain significance
embB	4248736	c.2223G>T	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
ethA	4326749	p.Asn242Thr	missense_variant	1.0	ethionamide	Uncertain significance
ethA	4327289	p.Leu62Gln	missense_variant	1.0	ethionamide	Uncertain significance
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	4338600	c.-79T>C	upstream_gene_variant	1.0	capreomycin	Uncertain significance
					amikacin	Uncertain significance
					kanamycin	Uncertain significance
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
gid	4408054	p.Leu50Arg	missense_variant	1.0	streptomycin	Uncertain significance
gid	4408156	p.Leu16Arg	missense_variant	0.99	streptomycin	Not assoc w R