TB-Profiler

TB-Profiler result

Run: SRR10040427

Summary

Run ID: SRR10040427

Sample name:

Date: 2024-10-05T02:09:51.993572

Number of reads: 5066265

Percentage reads mapped: 99.42

Median coverage: 146.0

Strain: lineage4.5

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
lineage4.5	Euro-American	RD122	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	ahpC	c.-54C>T	Uncertain significance	Mutation from literature
ethambutol	embB	p.Asp1024Asn	Uncertain significance	Mutation from literature
pyrazinamide	pncA	c.-11A>G	Assoc w R
streptomycin
fluoroquinolones
moxifloxacin	gyrA	p.Ala90Val	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin	gyrA	p.Ala90Val	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	7570	p.Ala90Val	missense_variant	0.99	levofloxacin	Assoc w R
gyrA	7570	p.Ala90Val	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)
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
pncA	2289252	c.-11A>G	upstream_gene_variant	1.0	pyrazinamide	Assoc w R
ahpC	2726139	c.-54C>T	upstream_gene_variant	1.0	isoniazid	Uncertain significance	Mutation from literature
embB	4249583	p.Asp1024Asn	missense_variant	1.0	ethambutol	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
gyrB	4949	c.-291G>C	upstream_gene_variant	1.0	levofloxacin
gyrB	4949	c.-291G>C	upstream_gene_variant	1.0	moxifloxacin
gyrB	6757	p.Ile506Met	missense_variant	1.0	levofloxacin	Uncertain significance
gyrB	6757	p.Ile506Met	missense_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	7892	c.591G>A	synonymous_variant	0.99	levofloxacin	Not assoc w R - Interim
gyrA	7892	c.591G>A	synonymous_variant	0.99	moxifloxacin	Not assoc w R - Interim
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
ccsA	620029	c.139C>T	synonymous_variant	1.0	kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R - Interim
					amikacin	Not assoc w R - Interim
rpoC	764840	p.Ile491Val	missense_variant	1.0	rifampicin	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	0.99	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	0.99	clofazimine	Not assoc w R
rpsL	781307	c.-253C>A	upstream_gene_variant	1.0	streptomycin
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1253860	p.Lys225Asn	missense_variant	0.99	levofloxacin	Uncertain significance
					moxifloxacin
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					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	2101701	c.1342C>T	synonymous_variant	0.99	isoniazid	Not assoc w R - Interim
					delamanid
					ethionamide	Not assoc w R - Interim
katG	2155546	p.Asp189Gly	missense_variant	1.0	isoniazid	Uncertain significance
PPE35	2170568	p.Ile15Met	missense_variant	1.0	pyrazinamide	Not assoc w R
Rv1979c	2221722	c.1443C>T	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2221722	c.1443C>T	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
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	3064876	p.Ser439Phe	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
rpoA	3878575	c.-68C>T	upstream_gene_variant	1.0	rifampicin	Not assoc w R
rpoA	3879070	c.-563G>A	upstream_gene_variant	1.0	rifampicin
clpC1	4038318	p.Pro796Leu	missense_variant	1.0	pyrazinamide	Not assoc w R
clpC1	4039040	c.1665C>T	synonymous_variant	1.0	pyrazinamide
embC	4242643	c.2781C>T	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