TB-Profiler

TB-Profiler result

Run: SRR1173525

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: SRR1173525

Sample name:

Date: 2024-10-04T15:11:05.854131

Number of reads: 326619

Percentage reads mapped: 92.57

Median coverage: 6.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	0.53
lineage2.2	East-Asian (Beijing)	RD105;RD207	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
fgd1	491742	c.960T>C	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
Rv1129c	1254562	c.-28T>C	upstream_gene_variant	1.0	levofloxacin	Not assoc w R
					moxifloxacin	Not assoc w R
					isoniazid	Not assoc w R
					rifampicin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rpsA	1834177	c.636A>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Not assoc w R