TB-Profiler

TB-Profiler result

Run: SRR1175040

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: SRR1175040

Sample name:

Date: 2024-10-05T11:38:07.140703

Number of reads: 329549

Percentage reads mapped: 96.61

Median coverage: 6.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Other

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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	0.51
lineage4	Euro-American	None	1.0
lineage4.3.3	Euro-American (LAM)	RD115	0.53

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
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	ethA	c.-11A>G	Uncertain significance	Mutation from literature
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
ethA	4327484	c.-11A>G	upstream_gene_variant	1.0	ethionamide	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	Confidence
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1476056	n.2399G>A	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1476056	n.2399G>A	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv2752c	3065824	p.Pro123Leu	missense_variant	1.0	levofloxacin	Not assoc w R
					moxifloxacin	Uncertain significance
					isoniazid	Not assoc w R - Interim
					rifampicin	Not assoc w R
					ethambutol	Not assoc w R
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine