TB-Profiler

TB-Profiler result

Run: ERR4822198

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: ERR4822198

Sample name:

Date: 2024-10-05T04:38:33.505408

Number of reads: 253426

Percentage reads mapped: 89.22

Median coverage: 5.0

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	0.46
lineage4	Euro-American	None	1.0
lineage4.3.3	Euro-American (LAM)	RD115	0.3

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
dnaA	919	p.Pro307Ser	missense_variant	1.0	isoniazid	Uncertain significance
rrs	1472781	n.936C>T	non_coding_transcript_exon_variant	0.9	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472793	n.948A>T	non_coding_transcript_exon_variant	0.91	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472803	n.958T>A	non_coding_transcript_exon_variant	0.82	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rpsA	1834836	p.Met432Thr	missense_variant	1.0	pyrazinamide	Not assoc w R - Interim
thyA	3073868	p.Thr202Ala	missense_variant	1.0	para-aminosalicylic_acid