TB-Profiler

TB-Profiler result

Run: SRR11972162

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: SRR11972162

Sample name:

Date: 2024-04-15T02:46:33.469778

Number of reads: 579310

Percentage reads mapped: 99.25

Median coverage: 11.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: HR-TB

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

Lineage	Family	RDs	Frequency
lineage4.1	Euro-American	None	1.0
lineage4.1.1.1	Euro-American (X-type)	RD183	0.68
lineage4	Euro-American	None	1.0
lineage4.1.1	Euro-American (X-type)	None	0.99

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol
pyrazinamide
streptomycin
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
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R	High-level resistance

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
Rv0010c	13166	c.393C>A	synonymous_variant	1.0	isoniazid
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1254511	c.24G>A	synonymous_variant	1.0	moxifloxacin
					levofloxacin
					rifampicin
					isoniazid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472193	n.348A>G	non_coding_transcript_exon_variant	0.14	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1472214	n.369C>G	non_coding_transcript_exon_variant	0.4	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472225	n.380C>A	non_coding_transcript_exon_variant	0.42	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					amikacin	Uncertain significance
rrs	1472235	n.390G>C	non_coding_transcript_exon_variant	0.34	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472240	n.395G>C	non_coding_transcript_exon_variant	0.26	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
rrs	1472242	n.397C>T	non_coding_transcript_exon_variant	0.21	streptomycin	Uncertain significance
					kanamycin
					capreomycin
					amikacin
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin	Not assoc w R
PPE35	2170048	p.Leu189Val	missense_variant	0.4	pyrazinamide
PPE35	2170053	p.Thr187Ser	missense_variant	0.43	pyrazinamide
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
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
lpqB	3623744	c.1167C>T	synonymous_variant	1.0	bedaquiline
lpqB	3623744	c.1167C>T	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
fbiA	3641447	p.Thr302Met	missense_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Uncertain significance
rpoA	3877553	p.Glu319Lys	missense_variant	1.0	rifampicin	Not assoc w R
embC	4240897	c.1035C>G	synonymous_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embB	4249408	c.2895G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
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	4407995	p.Ser70Arg	missense_variant	1.0	streptomycin	Uncertain significance