TB-Profiler

TB-Profiler result

Run: ERR1465952

Summary

Run ID: ERR1465952

Sample name:

Date: 2024-10-03T23:38:17.555074

Number of reads: 6748472

Percentage reads mapped: 99.93

Median coverage: 127.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	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
isoniazid
ethambutol
pyrazinamide
streptomycin
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

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	7704	p.Thr135Ala	missense_variant	1.0	levofloxacin
gyrA	7704	p.Thr135Ala	missense_variant	1.0	moxifloxacin
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
ribD	2987070	p.Ala78Thr	missense_variant	1.0	para-aminosalicylic_acid
Rv3083	3449713	p.Ala404Thr	missense_variant	1.0	ethionamide	Uncertain significance
panD	4045234	c.-953G>C	upstream_gene_variant	1.0	pyrazinamide
glpK	4138622	c.1134C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					isoniazid	Not assoc w R
					streptomycin	Not assoc w R - Interim
					rifampicin	Not assoc w R
					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