TB-Profiler

TB-Profiler result

Run: SRR1180474

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: SRR1180474

Sample name:

Date: 2024-10-05T14:18:06.319179

Number of reads: 1853

Percentage reads mapped: 0.65

Median coverage: 0.0

Strain: 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
lineage4.9	Euro-American (H37Rv-like)	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
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.68	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.68	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.85	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.85	linezolid	Uncertain significance
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.76	capreomycin
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.76	linezolid
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1476368	n.2711T>C	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.77	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.77	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.32	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.32	linezolid	Uncertain significance
rrl	1476381	n.2724G>A	non_coding_transcript_exon_variant	0.71	capreomycin
rrl	1476381	n.2724G>A	non_coding_transcript_exon_variant	0.71	linezolid
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	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.42	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.42	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.49	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.49	linezolid
rrl	1476417	n.2760T>C	non_coding_transcript_exon_variant	0.46	capreomycin	Uncertain significance
rrl	1476417	n.2760T>C	non_coding_transcript_exon_variant	0.46	linezolid
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1476428	n.2771C>A	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.25	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.48	capreomycin
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.48	linezolid
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.48	capreomycin
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.48	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.41	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.41	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.55	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.55	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance