TB-Profiler

TB-Profiler result

Run: SRR8692822

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: SRR8692822

Sample name:

Date: 2024-10-04T00:58:18.768597

Number of reads: 1287619

Percentage reads mapped: 40.44

Median coverage: 29.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	0.98

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

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid	rplC	p.Cys154Arg	Assoc w R

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
rplC	801268	p.Cys154Arg	missense_variant	0.88	linezolid	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
rpoC	764746	c.1377G>T	synonymous_variant	0.27	rifampicin	Not assoc w R - Interim
rpoC	764752	c.1383G>C	synonymous_variant	0.29	rifampicin	Not assoc w R - Interim
Rv1258c	1406686	p.Val219Ile	missense_variant	0.97	streptomycin
					pyrazinamide
					isoniazid
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	0.5	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrl	1474552	n.895C>T	non_coding_transcript_exon_variant	0.53	capreomycin
rrl	1474552	n.895C>T	non_coding_transcript_exon_variant	0.53	linezolid
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.26	capreomycin	Not assoc w R
rrl	1475988	n.2331A>G	non_coding_transcript_exon_variant	0.26	linezolid	Uncertain significance
rrl	1475991	n.2334T>C	non_coding_transcript_exon_variant	0.27	capreomycin	Uncertain significance
rrl	1475991	n.2334T>C	non_coding_transcript_exon_variant	0.27	linezolid
rrl	1475995	n.2338G>A	non_coding_transcript_exon_variant	0.27	capreomycin	Uncertain significance
rrl	1475995	n.2338G>A	non_coding_transcript_exon_variant	0.27	linezolid
rrl	1476030	n.2373A>G	non_coding_transcript_exon_variant	0.31	capreomycin	Uncertain significance
rrl	1476030	n.2373A>G	non_coding_transcript_exon_variant	0.31	linezolid
rrl	1476032	n.2375C>A	non_coding_transcript_exon_variant	0.28	capreomycin
rrl	1476032	n.2375C>A	non_coding_transcript_exon_variant	0.28	linezolid
rrl	1476034	n.2377C>G	non_coding_transcript_exon_variant	0.32	capreomycin	Uncertain significance
rrl	1476034	n.2377C>G	non_coding_transcript_exon_variant	0.32	linezolid
rrl	1476035	n.2378G>C	non_coding_transcript_exon_variant	0.32	capreomycin	Uncertain significance
rrl	1476035	n.2378G>C	non_coding_transcript_exon_variant	0.32	linezolid
rrl	1476044	n.2387T>G	non_coding_transcript_exon_variant	0.29	capreomycin	Uncertain significance
rrl	1476044	n.2387T>G	non_coding_transcript_exon_variant	0.29	linezolid
rrl	1476045	n.2388G>T	non_coding_transcript_exon_variant	0.29	capreomycin	Uncertain significance
rrl	1476045	n.2388G>T	non_coding_transcript_exon_variant	0.29	linezolid
rrl	1476047	n.2390G>T	non_coding_transcript_exon_variant	0.29	capreomycin
rrl	1476047	n.2390G>T	non_coding_transcript_exon_variant	0.29	linezolid
rrl	1476049	n.2392C>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476049	n.2392C>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476056	n.2399G>A	non_coding_transcript_exon_variant	0.33	capreomycin	Not assoc w R
rrl	1476056	n.2399G>A	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	0.31	kanamycin	Not assoc w R
					capreomycin	Not assoc w R
					amikacin	Not assoc w R