TB-Profiler

TB-Profiler result

Run: ERR1035355

Summary

Run ID: ERR1035355

Sample name:

Date: 2024-10-05T01:39:44.049037

Number of reads: 4209555

Percentage reads mapped: 96.79

Median coverage: 40.0

Strain: lineage4.6.4

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON

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

Lineage	Family	RDs	Frequency
lineage4.6	Euro-American	None	0.99
lineage4.6.4	Euro-American	None	0.99
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	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Val	Assoc w R
pyrazinamide	pncA	p.Thr76Pro	Assoc w R
streptomycin
fluoroquinolones
moxifloxacin	gyrA	p.Asp94Gly	Assoc w R	High-level resistance
ofloxacin
levofloxacin	gyrA	p.Asp94Gly	Assoc w R
ciprofloxacin
aminoglycosides
amikacin	rrs	n.1401A>G	Assoc w R
capreomycin	rrs	n.1401A>G	Assoc w R
kanamycin	rrs	n.1401A>G	Assoc w R
cycloserine	alr	p.Met343Thr		Mutation from literature
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.Asp94Gly	missense_variant	1.0	levofloxacin	Assoc w R
gyrA	7582	p.Asp94Gly	missense_variant	1.0	moxifloxacin	Assoc w R	High-level resistance
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	1.0	amikacin	Assoc w R
					capreomycin	Assoc w R
					kanamycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2289016	p.Thr76Pro	missense_variant	0.95	pyrazinamide	Assoc w R
alr	3840393	p.Met343Thr	missense_variant	0.5	cycloserine		Mutation from literature
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
dnaA	29	p.Thr10Ser	missense_variant	1.0	isoniazid	Uncertain significance
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
Rv0010c	13569	c.-11C>A	upstream_gene_variant	1.0	isoniazid	Uncertain significance
rpoB	762715	p.Val970Ala	missense_variant	1.0	rifampicin	Uncertain significance
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
Rv1129c	1254144	p.Thr131Pro	missense_variant	1.0	levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					isoniazid	Uncertain significance
					rifampicin	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1474140	n.483C>T	non_coding_transcript_exon_variant	0.15	capreomycin	Uncertain significance
rrl	1474140	n.483C>T	non_coding_transcript_exon_variant	0.15	linezolid	Uncertain significance
rrl	1474750	n.1093C>T	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1474750	n.1093C>T	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
inhA	1674685	p.Thr162Ala	missense_variant	1.0	isoniazid
inhA	1674685	p.Thr162Ala	missense_variant	1.0	ethionamide
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	2156724	c.-613C>T	upstream_gene_variant	1.0	isoniazid
Rv1979c	2222795	p.Asp124Asn	missense_variant	0.97	bedaquiline
Rv1979c	2222795	p.Asp124Asn	missense_variant	0.97	clofazimine
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	0.96	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	0.96	clofazimine	Not assoc w R
pncA	2288792	c.450C>T	synonymous_variant	1.0	pyrazinamide
eis	2714393	p.Val314Leu	missense_variant	1.0	kanamycin	Uncertain significance
eis	2714393	p.Val314Leu	missense_variant	1.0	amikacin	Uncertain significance
Rv2477c	2783928	p.Pro39Ser	missense_variant	0.97	kanamycin	Uncertain significance
					levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					streptomycin	Uncertain significance
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
					amikacin	Uncertain significance
lpqB	3625390	c.-480C>T	upstream_gene_variant	1.0	rifampicin
lpqB	3625390	c.-480C>T	upstream_gene_variant	1.0	bedaquiline
rpoA	3878745	c.-238C>G	upstream_gene_variant	1.0	rifampicin	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ethA	4326693	p.Arg261Trp	missense_variant	1.0	ethionamide	Uncertain significance
whiB6	4338546	c.-25G>C	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
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
gid	4407946	p.Leu86Pro	missense_variant	1.0	streptomycin	Uncertain significance