TB-Profiler

TB-Profiler result

Run: SRR6785230

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: SRR6785230

Sample name:

Date: 2024-10-03T20:52:31.957558

Number of reads: 666971

Percentage reads mapped: 99.68

Median coverage: 6.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: Other

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	0.68
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	0.55
lineage2.2	East-Asian (Beijing)	RD105;RD207	0.68
lineage4	Euro-American	None	0.44

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin
isoniazid
ethambutol	embB	p.Gly406Ser	Assoc w R
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
embB	4247729	p.Gly406Ser	missense_variant	0.9	ethambutol	Assoc w R

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
ccsA	620625	p.Ile245Met	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
embA	4243460	c.228C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338371	p.Thr51Pro	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	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