TB-Profiler

TB-Profiler result

Run: SRR1173514

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: SRR1173514

Sample name:

Date: 2024-10-03T22:30:28.278195

Number of reads: 299718

Percentage reads mapped: 96.11

Median coverage: 6.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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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	1.0
lineage4	Euro-American	None	1.0
lineage4.3.3	Euro-American (LAM)	RD115	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	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
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
gid	4408156	p.Leu16Arg	missense_variant	1.0	streptomycin	Not assoc w R