TB-Profiler

TB-Profiler result

Run: ERR2229233

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: ERR2229233

Sample name:

Date: 2024-10-04T17:36:54.052874

Number of reads: 136667

Percentage reads mapped: 50.69

Median coverage: 3.0

Strain: lineage4.8;lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.8	Euro-American (mainly T)	RD219	0.12
lineage4.9	Euro-American (H37Rv-like)	None	0.85

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
rrs	1473262	n.1417T>C	non_coding_transcript_exon_variant	0.91	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473276	n.1431A>C	non_coding_transcript_exon_variant	0.9	kanamycin
					capreomycin
					streptomycin
					amikacin
rrl	1474498	n.841G>T	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1474498	n.841G>T	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1474505	n.848C>G	non_coding_transcript_exon_variant	0.69	capreomycin	Uncertain significance
rrl	1474505	n.848C>G	non_coding_transcript_exon_variant	0.69	linezolid	Uncertain significance
rrl	1474508	n.851C>T	non_coding_transcript_exon_variant	0.69	capreomycin	Uncertain significance
rrl	1474508	n.851C>T	non_coding_transcript_exon_variant	0.69	linezolid	Uncertain significance
rrl	1474516	n.859C>A	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1474516	n.859C>A	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1474529	n.872A>C	non_coding_transcript_exon_variant	0.82	capreomycin
rrl	1474529	n.872A>C	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1474530	n.873G>A	non_coding_transcript_exon_variant	0.82	capreomycin
rrl	1474530	n.873G>A	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1474537	n.880G>A	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1474537	n.880G>A	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1474539	n.882C>T	non_coding_transcript_exon_variant	0.69	capreomycin
rrl	1474539	n.882C>T	non_coding_transcript_exon_variant	0.69	linezolid
rrl	1474540	n.883T>G	non_coding_transcript_exon_variant	0.69	capreomycin
rrl	1474540	n.883T>G	non_coding_transcript_exon_variant	0.69	linezolid
rrl	1474794	n.1137C>T	non_coding_transcript_exon_variant	0.7	capreomycin	Uncertain significance
rrl	1474794	n.1137C>T	non_coding_transcript_exon_variant	0.7	linezolid	Uncertain significance
rrl	1475883	n.2226A>C	non_coding_transcript_exon_variant	0.88	capreomycin	Uncertain significance
rrl	1475883	n.2226A>C	non_coding_transcript_exon_variant	0.88	linezolid
rrl	1475892	n.2235A>C	non_coding_transcript_exon_variant	0.88	capreomycin
rrl	1475892	n.2235A>C	non_coding_transcript_exon_variant	0.88	linezolid
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1475898	n.2241A>G	non_coding_transcript_exon_variant	0.83	linezolid
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475899	n.2242G>A	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475900	n.2243A>G	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475900	n.2243A>G	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1475916	n.2259C>T	non_coding_transcript_exon_variant	0.83	capreomycin	Uncertain significance
rrl	1475916	n.2259C>T	non_coding_transcript_exon_variant	0.83	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	1.0	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance