TB-Profiler

TB-Profiler result

Run: ERR4797441

Summary

Run ID: ERR4797441

Sample name:

Date: 2024-10-03T23:54:00.388700

Number of reads: 3370212

Percentage reads mapped: 99.51

Median coverage: 98.0

Strain: lineage4.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.2.2	Euro-American (Ural)	None	0.99
lineage4.2	Euro-American	None	1.0
lineage4	Euro-American	None	1.0
lineage4.2.2.2	Euro-American (Ural)	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.His445Asp	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
isoniazid	ahpC	c.-52C>T	Uncertain significance	Mutation from literature
ethambutol	embB	p.Met306Val	Assoc w R
pyrazinamide	pncA	p.Trp119Arg	Assoc w R - Interim
streptomycin	rrs	n.514A>C	Assoc w R
streptomycin	gid	c.102delG	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
rpoB	761139	p.His445Asp	missense_variant	1.0	rifampicin	Assoc w R
rrs	1472359	n.514A>C	non_coding_transcript_exon_variant	1.0	streptomycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
pncA	2288887	p.Trp119Arg	missense_variant	1.0	pyrazinamide	Assoc w R - Interim
ahpC	2726141	c.-52C>T	upstream_gene_variant	1.0	isoniazid	Uncertain significance	Mutation from literature
embB	4247429	p.Met306Val	missense_variant	1.0	ethambutol	Assoc w R
gid	4408100	c.102delG	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
gyrB	5965	c.726A>G	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrB	5965	c.726A>G	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
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	7521	p.Ala74Thr	missense_variant	1.0	levofloxacin	Uncertain significance
gyrA	7521	p.Ala74Thr	missense_variant	1.0	moxifloxacin	Uncertain significance
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	8688	p.Ala463Ser	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	8688	p.Ala463Ser	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
gyrA	9328	p.Ala676Val	missense_variant	1.0	levofloxacin	Uncertain significance
gyrA	9328	p.Ala676Val	missense_variant	1.0	moxifloxacin	Uncertain significance
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
Rv0565c	657425	p.Gly16Ser	missense_variant	1.0	ethionamide	Uncertain significance
rpoB	761489	c.1683G>A	synonymous_variant	1.0	rifampicin	Not assoc w R
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
Rv1129c	1254563	c.-29A>C	upstream_gene_variant	0.1	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
fbiC	1305180	c.2250G>A	synonymous_variant	1.0	pretomanid
					delamanid	Not assoc w R - Interim
					clofazimine	Not assoc w R - Interim
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
lpqB	3623459	c.1452G>A	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
lpqB	3623459	c.1452G>A	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ethA	4326581	p.Asn298Thr	missense_variant	1.0	ethionamide	Uncertain significance
whiB6	4338513	c.9C>T	synonymous_variant	1.0	kanamycin	Not assoc w R - Interim
					capreomycin	Not assoc w R - Interim
					amikacin	Not assoc w R - Interim
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