TB-Profiler

TB-Profiler result

Run: ERR4820399

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: ERR4820399

Sample name:

Date: 2024-04-16T09:57:32.498055

Number of reads: 373957

Percentage reads mapped: 77.66

Median coverage: 5.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage4.6	Euro-American	None	1.0
lineage4.6.2	Euro-American	RD726	1.0
lineage4.6.2.2	Euro-American (Cameroon)	RD726	0.37
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
isoniazid	inhA	c.-777C>T	Assoc w R	Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	inhA	c.-777C>T	Assoc w R	Alias fabG1_c.-15C>T
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
inhA	1673425	c.-777C>T	upstream_gene_variant	1.0	ethionamide	Assoc w R	Alias fabG1_c.-15C>T
inhA	1673425	c.-777C>T	upstream_gene_variant	1.0	isoniazid	Assoc w R	Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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
mmpL5	778298	c.183G>A	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
mmpL5	778298	c.183G>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin