TB-Profiler

TB-Profiler result

Run: ERR2503468

Summary

Run ID: ERR2503468

Sample name:

Date: 2024-04-15T23:44:30.975529

Number of reads: 1597024

Percentage reads mapped: 99.58

Median coverage: 51.0

Strain: lineage4.4

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
lineage4.4	Euro-American	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	gid	c.346_347insT	Assoc w R
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
gid	4407856	c.346_347insT	frameshift_variant	1.0	streptomycin	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
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	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	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
rpoB	762914	c.3108C>T	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1258c	1407014	p.Leu109Phe	missense_variant	1.0	streptomycin
					isoniazid	Uncertain significance
					pyrazinamide	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2169265	p.Ser450Arg	missense_variant	1.0	pyrazinamide	Uncertain significance
Rv1979c	2223271	c.-107G>A	upstream_gene_variant	1.0	clofazimine	Uncertain significance
Rv1979c	2223271	c.-107G>A	upstream_gene_variant	1.0	bedaquiline	Uncertain significance
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv2477c	2783159	p.Ala295Val	missense_variant	1.0	ethambutol	Uncertain significance
					moxifloxacin
					streptomycin
					levofloxacin
					kanamycin
					rifampicin	Uncertain significance
					amikacin
Rv2752c	3065715	c.477T>C	synonymous_variant	1.0	ethambutol	Not assoc w R - Interim
					moxifloxacin	Not assoc w R - Interim
					levofloxacin	Not assoc w R - Interim
					rifampicin	Not assoc w R - Interim
					isoniazid	Not assoc w R - Interim
Rv2752c	3066452	c.-261T>G	upstream_gene_variant	1.0	ethambutol
					moxifloxacin
					levofloxacin
					rifampicin
					isoniazid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
embC	4238963	c.-900C>T	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4268928	c.906C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269375	c.459G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
ethA	4328200	c.-727C>T	upstream_gene_variant	1.0	ethionamide
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin