TB-Profiler

TB-Profiler result

Run: SRR26056417

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: SRR26056417

Sample name:

Date: 2024-10-03T14:36:15.858115

Number of reads: 344050

Percentage reads mapped: 90.36

Median coverage: 9.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	1.0
lineage4.1.1.1	Euro-American (X-type)	RD183	0.62
lineage4	Euro-American	None	1.0
lineage4.1.1	Euro-American (X-type)	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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1476055	n.2398C>T	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476055	n.2398C>T	non_coding_transcript_exon_variant	1.0	linezolid
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.58	linezolid	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476245	n.2588C>T	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
ahpC	2726210	c.18T>C	synonymous_variant	1.0	isoniazid	Not assoc w R - Interim
embC	4240897	c.1035C>G	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4249408	c.2895G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin