TB-Profiler

TB-Profiler result

Run: SRR21700950

Summary

Run ID: SRR21700950

Sample name:

Date: 2024-10-05T07:59:08.565695

Number of reads: 6380151

Percentage reads mapped: 99.98

Median coverage: 215.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin	gyrB	p.Asp461Asn	Assoc w R - Interim	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
moxifloxacin	gyrB	p.Ala504Thr	Uncertain significance	Mutation from literature
ofloxacin
levofloxacin	gyrB	p.Asp461Asn	Assoc w R
levofloxacin	gyrB	p.Ala504Thr	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
gyrB	6620	p.Asp461Asn	missense_variant	1.0	levofloxacin	Assoc w R
gyrB	6620	p.Asp461Asn	missense_variant	1.0	moxifloxacin	Assoc w R - Interim	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrB	6749	p.Ala504Thr	missense_variant	1.0	levofloxacin	Uncertain significance	Mutation from literature
gyrB	6749	p.Ala504Thr	missense_variant	1.0	moxifloxacin	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
Rv1258c	1406686	p.Val219Ile	missense_variant	1.0	streptomycin
					pyrazinamide
					isoniazid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rpoA	3878619	c.-112A>C	upstream_gene_variant	0.14	rifampicin
embB	4247039	p.Phe176Val	missense_variant	0.11	ethambutol