TB-Profiler

TB-Profiler result

Run: ERR4812866

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: ERR4812866

Sample name:

Date: 2024-10-04T16:28:37.817519

Number of reads: 274372

Percentage reads mapped: 99.39

Median coverage: 5.0

Strain: lineage4.3.3;lineage4.9

Spoligotype:

Drug-resistance: HR-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	0.17
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	0.75
lineage4.3.3	Euro-American (LAM)	RD115	0.58

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
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
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance

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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
PPE35	2168998	p.Ile539Val	missense_variant	0.88	pyrazinamide	Uncertain significance
Rv2477c	2783921	p.Gly41Glu	missense_variant	1.0	kanamycin	Uncertain significance
					levofloxacin	Uncertain significance
					moxifloxacin	Uncertain significance
					streptomycin	Uncertain significance
					rifampicin	Not assoc w R
					ethambutol	Uncertain significance
					amikacin	Uncertain significance
thyA	3073868	p.Thr202Ala	missense_variant	1.0	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
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