TB-Profiler

TB-Profiler result

Run: SRR1169168

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: SRR1169168

Sample name:

Date: 2024-04-15T00:29:11.643462

Number of reads: 1002331

Percentage reads mapped: 98.1

Median coverage: 22.0

Strain: lineage4.3.4.2.1;lineage4.4.1.1.1

Spoligotype:

Drug-resistance: MDR-TB

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

Lineage	Family	RDs	Frequency
lineage4.3	Euro-American (LAM)	None	0.55
lineage4.4.1.1.1	Euro-American	None	0.48
lineage4.4.1	Euro-American (S-type)	None	0.47
lineage4	Euro-American	None	1.0
lineage4.4.1.1	Euro-American	None	0.49
lineage4.3.4.2.1	Euro-American (LAM)	RD174	0.49
lineage4.3.4	Euro-American (LAM)	RD174	0.51
lineage4.4	Euro-American	None	0.47

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin	rpoB	p.His445Leu	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
ethambutol	embB	p.Gly406Ala	Assoc w R
pyrazinamide
streptomycin	rpsL	p.Lys43Arg	Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin	rrs	n.1401A>G	Assoc w R
capreomycin	rrs	n.1401A>G	Assoc w R
kanamycin	rrs	n.1401A>G	Assoc w R
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	761140	p.His445Leu	missense_variant	0.71	rifampicin	Assoc w R
rpsL	781687	p.Lys43Arg	missense_variant	0.58	streptomycin	Assoc w R
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	0.57	kanamycin	Assoc w R
					amikacin	Assoc w R
					capreomycin	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance
embB	4247431	p.Met306Ile	missense_variant	0.42	ethambutol	Assoc w R
embB	4247730	p.Gly406Ala	missense_variant	0.5	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	1391	p.Gln464Arg	missense_variant	0.41	isoniazid	Uncertain significance
gyrB	6140	p.Val301Leu	missense_variant	0.56	levofloxacin	Not assoc w R
gyrB	6140	p.Val301Leu	missense_variant	0.56	moxifloxacin	Not assoc w R
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	575538	p.Asp64Gly	missense_variant	0.71	ethionamide
mshA	575538	p.Asp64Gly	missense_variant	0.71	isoniazid
rpoC	764744	p.Arg459Trp	missense_variant	0.45	rifampicin	Uncertain significance
rpoC	764995	c.1626C>G	synonymous_variant	0.36	rifampicin	Not assoc w R
rpoC	765494	p.Val709Leu	missense_variant	0.47	rifampicin
rpoC	766487	p.Pro1040Ser	missense_variant	0.61	rifampicin	Uncertain significance
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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tsnR	1853674	c.69G>A	synonymous_variant	0.5	linezolid	Not assoc w R - Interim
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
ndh	2102990	p.Val18Ala	missense_variant	0.67	ethionamide	Uncertain significance
					delamanid	Uncertain significance
					isoniazid	Not assoc w R
PPE35	2169840	p.Gly258Asp	missense_variant	0.59	pyrazinamide	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	0.94	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	0.94	bedaquiline	Not assoc w R - Interim
ribD	2986827	c.-12G>A	upstream_gene_variant	0.4	para-aminosalicylic_acid
Rv2752c	3064993	p.Trp400*	stop_gained	0.43	ethambutol	Uncertain significance
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					rifampicin	Uncertain significance
					isoniazid	Uncertain significance
thyA	3073868	p.Thr202Ala	missense_variant	0.41	para-aminosalicylic_acid
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3236c	3612009	p.Ala370Thr	missense_variant	0.64	pyrazinamide	Not assoc w R
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
alr	3840719	c.702A>G	synonymous_variant	0.54	cycloserine
embC	4238963	c.-900C>T	upstream_gene_variant	0.43	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269308	p.Phe176Leu	missense_variant	0.58	ethambutol	Uncertain significance
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
gid	4407714	p.Lys163Asn	missense_variant	0.4	streptomycin	Uncertain significance
gid	4408156	p.Leu16Arg	missense_variant	0.35	streptomycin	Not assoc w R