TB-Profiler

TB-Profiler result

Run: SRR8692807

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: SRR8692807

Sample name:

Date: 2024-10-04T00:58:13.987885

Number of reads: 821924

Percentage reads mapped: 51.12

Median coverage: 19.0

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	1.0	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
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472106	n.261G>A	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472108	n.263C>T	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472150	n.305T>A	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrl	1475753	n.2096C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475753	n.2096C>T	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475759	n.2102C>T	non_coding_transcript_exon_variant	0.82	capreomycin
rrl	1475759	n.2102C>T	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475762	n.2105G>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475762	n.2105G>T	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475764	n.2107A>C	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475764	n.2107A>C	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475765	n.2108A>G	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475765	n.2108A>G	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475775	n.2118G>A	non_coding_transcript_exon_variant	0.75	capreomycin	Uncertain significance
rrl	1475775	n.2118G>A	non_coding_transcript_exon_variant	0.75	linezolid
rrl	1476088	n.2431A>C	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1476088	n.2431A>C	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1476110	n.2453G>C	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1476110	n.2453G>C	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1476115	n.2458T>C	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1476115	n.2458T>C	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1476131	n.2474C>T	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1476131	n.2474C>T	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance