TB-Profiler

TB-Profiler result

Run: SRR19303792

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: SRR19303792

Sample name:

Date: 2024-04-16T03:33:33.145258

Number of reads: 319813

Percentage reads mapped: 9.33

Median coverage: 8.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.1.2	Euro-American	None	1.0
lineage4.1.2.1	Euro-American (Haarlem)	RD182	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
isoniazid
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

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
fgd1	491591	p.Lys270Met	missense_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Uncertain significance
rpoC	765150	p.Gly594Glu	missense_variant	1.0	rifampicin	Not assoc w R
rrl	1476356	n.2699C>G	non_coding_transcript_exon_variant	0.92	capreomycin
rrl	1476356	n.2699C>G	non_coding_transcript_exon_variant	0.92	linezolid
rrl	1476357	n.2700T>A	non_coding_transcript_exon_variant	0.92	capreomycin
rrl	1476357	n.2700T>A	non_coding_transcript_exon_variant	0.92	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1476384	n.2727G>C	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1476384	n.2727G>C	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.88	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.88	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.88	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.88	linezolid
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1476443	n.2786G>C	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1476443	n.2786G>C	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1476455	n.2798C>G	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1476455	n.2798C>G	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.88	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.88	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.87	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.87	linezolid	Uncertain significance
rrl	1476470	n.2813C>T	non_coding_transcript_exon_variant	0.93	capreomycin	Uncertain significance
rrl	1476470	n.2813C>T	non_coding_transcript_exon_variant	0.93	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.87	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.87	linezolid	Uncertain significance
pncA	2289128	c.114G>C	synonymous_variant	1.0	pyrazinamide	Not assoc w R - Interim
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R