TB-Profiler

TB-Profiler result

Run: ERR4423696

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: ERR4423696

Sample name:

Date: 2024-10-05T04:32:40.392854

Number of reads: 655602

Percentage reads mapped: 99.43

Median coverage: 10.0

Strain: lineage3.1.1

Spoligotype:

Drug-resistance: Other

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

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	1.0
lineage3.1.1	East-African-Indian	RD750	1.0

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

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin
isoniazid
ethambutol	embB	p.Gly406Ala	Assoc w R
pyrazinamide	pncA	c.-448_*4192del	Assoc w R
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
pncA	2284488	c.-448_*4192del	transcript_ablation	1.0	pyrazinamide	Assoc w R
embB	4247730	p.Gly406Ala	missense_variant	1.0	ethambutol	Assoc w R

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
rpoB	762434	c.2628T>G	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	767123	p.Val1252Met	missense_variant	1.0	rifampicin	Uncertain significance
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2170461	p.Gly51Glu	missense_variant	1.0	pyrazinamide	Not assoc w R
Rv2477c	2782498	c.1545C>T	synonymous_variant	1.0	kanamycin	Not assoc w R
					levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					rifampicin	Not assoc w R
					ethambutol	Not assoc w R
					amikacin	Not assoc w R
Rv2477c	2783814	p.Pro77Ser	missense_variant	1.0	kanamycin
					levofloxacin
					moxifloxacin
					streptomycin
					rifampicin	Uncertain significance
					ethambutol	Uncertain significance
					amikacin
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R