TB-Profiler

TB-Profiler result

Run: SRR11972220

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: SRR11972220

Sample name:

Date: 2024-10-04T00:25:03.834756

Number of reads: 307603

Percentage reads mapped: 99.45

Median coverage: 10.0

Strain: lineage2.2.1.1

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	1.0
lineage2.2.1.1	East-Asian (Beijing)	RD105;RD207;RD181;RD150	0.99

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
gyrA	7362	p.Glu21Gln	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
fgd1	491742	c.960T>C	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R
ccsA	620625	p.Ile245Met	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Not assoc w R
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	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
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
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
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
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
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4243460	c.228C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4248115	c.1602C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338594	c.-73T>G	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
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