TB-Profiler

TB-Profiler result

Run: SRR3610865

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: SRR3610865

Sample name:

Date: 2024-10-05T06:27:27.828803

Number of reads: 90645

Percentage reads mapped: 89.3

Median coverage: 0.0

Strain: lineage4.9

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	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	rpoB	p.Ser450Leu	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide
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)
moxifloxacin	gyrA	p.Asp94Val	Uncertain significance	Mutation from literature
ofloxacin
levofloxacin	gyrA	p.Asp94Ala	Assoc w R
levofloxacin	gyrA	p.Asp94Val	Uncertain significance	Mutation from literature
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	0.43	levofloxacin	Assoc w R
gyrA	7582	p.Asp94Ala	missense_variant	0.43	moxifloxacin	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA	7582	p.Asp94Val	missense_variant	0.52	levofloxacin	Uncertain significance	Mutation from literature
gyrA	7582	p.Asp94Val	missense_variant	0.52	moxifloxacin	Uncertain significance	Mutation from literature
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

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	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
eis	2715344	c.-12C>T	upstream_gene_variant	0.87	kanamycin	Assoc w R
eis	2715344	c.-12C>T	upstream_gene_variant	0.87	amikacin	Not assoc w R