TB-Profiler

TB-Profiler result

Run: DRR130212

Summary

Run ID: DRR130212

Sample name:

Date: 2024-10-05T05:40:35.303542

Number of reads: 3022988

Percentage reads mapped: 99.18

Median coverage: 163.0

Strain: lineage4.2.2

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON

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

Lineage	Family	RDs	Frequency
lineage4.2.2	Euro-American (Ural)	None	1.0
lineage4.2	Euro-American	None	1.0
lineage4	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	rpoB	p.Ser450Trp	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide
streptomycin	gid	p.Asp67His	Assoc w R - Interim
fluoroquinolones
moxifloxacin	gyrA	p.Ala90Val	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin	gyrA	p.Ala90Val	Assoc w R
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
gyrA	7570	p.Ala90Val	missense_variant	1.0	levofloxacin	Assoc w R
gyrA	7570	p.Ala90Val	missense_variant	1.0	moxifloxacin	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB	761155	p.Ser450Trp	missense_variant	1.0	rifampicin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
gid	4408004	p.Asp67His	missense_variant	1.0	streptomycin	Assoc w R - Interim

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
gyrB	7121	p.Pro628Ala	missense_variant	1.0	levofloxacin	Uncertain significance
gyrB	7121	p.Pro628Ala	missense_variant	1.0	moxifloxacin	Uncertain significance
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
mshA	576077	c.730C>T	synonymous_variant	1.0	isoniazid	Not assoc w R
mshA	576077	c.730C>T	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
rplC	800204	c.-605T>C	upstream_gene_variant	1.0	linezolid
rplC	801256	p.Ser150Ala	missense_variant	1.0	linezolid
fbiC	1303085	p.Gly52Asp	missense_variant	1.0	pretomanid
					delamanid
					clofazimine
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					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
bacA	2063685	c.1044G>A	synonymous_variant	1.0	kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					amikacin	Not assoc w R
bacA	2063911	p.Ile273Thr	missense_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	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
Rv2752c	3066280	c.-89C>T	upstream_gene_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
					ethambutol
ald	3086742	c.-78A>C	upstream_gene_variant	1.0	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
clpC1	4039140	p.Glu522Gly	missense_variant	1.0	pyrazinamide
glpK	4139588	c.168G>A	synonymous_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					streptomycin
					rifampicin
					ethambutol
embC	4239334	c.-529T>C	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4244400	p.Leu390Met	missense_variant	1.0	ethambutol	Uncertain significance
embA	4244549	c.1317C>A	synonymous_variant	1.0	ethambutol
embB	4247463	p.Ser317Tyr	missense_variant	1.0	ethambutol
embB	4249533	p.Ala1007Val	missense_variant	1.0	ethambutol	Uncertain significance
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