TB-Profiler

TB-Profiler result

Run: ERR867543

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: ERR867543

Sample name:

Date: 2024-03-24T19:22:11.508969

Number of reads: 305422

Percentage reads mapped: 19.16

Median coverage: 10.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.6	Euro-American	None	0.86
lineage4.6.2.2	Euro-American (Cameroon)	RD726	0.12
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
ethambutol
pyrazinamide
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

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	0.67	clofazimine	Not assoc w R - Interim
mmpL5	778298	c.183G>A	synonymous_variant	0.67	bedaquiline	Not assoc w R - Interim
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472969	n.1124A>G	non_coding_transcript_exon_variant	0.46	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472970	n.1125C>G	non_coding_transcript_exon_variant	0.46	streptomycin
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.46	capreomycin	Uncertain significance
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.46	linezolid
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.63	capreomycin	Not assoc w R
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.63	linezolid	Uncertain significance
rrl	1476025	n.2368G>T	non_coding_transcript_exon_variant	0.71	capreomycin
rrl	1476025	n.2368G>T	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476030	n.2373A>G	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1476030	n.2373A>G	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476032	n.2375C>A	non_coding_transcript_exon_variant	0.71	capreomycin
rrl	1476032	n.2375C>A	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476033	n.2376T>C	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1476033	n.2376T>C	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476034	n.2377C>A	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1476034	n.2377C>A	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476045	n.2388G>T	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1476045	n.2388G>T	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476047	n.2390G>T	non_coding_transcript_exon_variant	0.71	capreomycin
rrl	1476047	n.2390G>T	non_coding_transcript_exon_variant	0.71	linezolid
rrl	1476049	n.2392C>T	non_coding_transcript_exon_variant	0.71	capreomycin	Uncertain significance
rrl	1476049	n.2392C>T	non_coding_transcript_exon_variant	0.71	linezolid	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476281	n.2624T>C	non_coding_transcript_exon_variant	0.58	linezolid	Uncertain significance
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin