TB-Profiler

TB-Profiler result

Run: SRR1183036

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: SRR1183036

Sample name:

Date: 2024-04-14T10:37:35.721906

Number of reads: 2202

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
rrs	1472779	n.934G>A	non_coding_transcript_exon_variant	0.67	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472803	n.958T>A	non_coding_transcript_exon_variant	0.92	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrl	1474839	n.1182C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1474839	n.1182C>T	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.42	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.42	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.76	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.76	linezolid	Uncertain significance
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.43	capreomycin
rrl	1476359	n.2702C>T	non_coding_transcript_exon_variant	0.43	linezolid
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.69	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.69	linezolid	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.6	capreomycin	Uncertain significance
rrl	1476372	n.2715T>C	non_coding_transcript_exon_variant	0.6	linezolid	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.56	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.56	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.39	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.39	linezolid
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.43	capreomycin	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.43	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.62	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.62	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.37	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.37	linezolid	Uncertain significance
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.35	capreomycin
rrl	1476443	n.2786G>A	non_coding_transcript_exon_variant	0.35	linezolid
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.34	capreomycin
rrl	1476455	n.2798C>T	non_coding_transcript_exon_variant	0.34	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.39	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.39	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.56	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.56	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
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	1.0	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	1.0	linezolid	Uncertain significance