TB-Profiler

TB-Profiler result

Run: SRR28389867

Summary

Run ID: SRR28389867

Sample name:

Date: 2024-05-22T08:21:51.017618

Number of reads: 3680098

Percentage reads mapped: 99.41

Median coverage: 101.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	1.0

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.Gln497Arg	Assoc w R
pyrazinamide
streptomycin	rrs	n.514A>C	Assoc w R
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
rrs	1472359	n.514A>C	non_coding_transcript_exon_variant	1.0	streptomycin	Assoc w R
embB	4248003	p.Gln497Arg	missense_variant	1.0	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
dnaA	1088	p.Ser363Asn	missense_variant	1.0	isoniazid	Uncertain significance
gyrA	7362	p.Glu21Gln	missense_variant	0.99	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	0.99	moxifloxacin	Not assoc w R
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rpsA	1834956	p.Ala472Val	missense_variant	1.0	pyrazinamide
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
ribD	2986956	p.Trp40Arg	missense_variant	1.0	para-aminosalicylic_acid
glpK	4138898	c.858T>C	synonymous_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					rifampicin
					isoniazid
aftB	4268017	p.Val274Leu	missense_variant	1.0	ethambutol
whiB6	4338593	c.-73delT	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
whiB6	4338596	c.-75G>C	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin