TB-Profiler

TB-Profiler result

Run: SRR2100149

Summary

Run ID: SRR2100149

Sample name:

Date: 2024-04-15T00:50:34.977862

Number of reads: 4755318

Percentage reads mapped: 99.73

Median coverage: 107.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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	Comment
rifampicin
isoniazid	inhA	c.-777C>T	Assoc w R	Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	inhA	c.-777C>T	Assoc w R	Alias fabG1_c.-15C>T
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
inhA	1673425	c.-777C>T	upstream_gene_variant	1.0	isoniazid	Assoc w R	Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA	1673425	c.-777C>T	upstream_gene_variant	1.0	ethionamide	Assoc w R	Alias fabG1_c.-15C>T

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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	0.98	capreomycin	Not assoc w R
fbiB	3640659	c.-876C>T	upstream_gene_variant	1.0	clofazimine
					pretomanid
					delamanid
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R