TB-Profiler

TB-Profiler result

Run: SRR7585435

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: SRR7585435

Sample name:

Date: 2025-02-11T17:15:54.680443

Number of reads: 34862

Percentage reads mapped: 4.53

Median coverage: 0.0

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	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	rrs	n.799C>T	Uncertain significance	Mutation from literature
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
rrs	1472644	n.799C>T	non_coding_transcript_exon_variant	0.8	streptomycin	Uncertain significance	Mutation from literature

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
rpoB	761057	c.1251G>C	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
rpoB	762929	c.3123G>C	synonymous_variant	0.69	rifampicin	Not assoc w R - Interim
rrs	1473110	n.1265T>G	non_coding_transcript_exon_variant	0.6	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473111	n.1266A>G	non_coding_transcript_exon_variant	0.6	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473145	n.1300C>T	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473166	n.1321G>A	non_coding_transcript_exon_variant	1.0	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1474777	n.1120T>C	non_coding_transcript_exon_variant	0.55	capreomycin	Not assoc w R
rrl	1474777	n.1120T>C	non_coding_transcript_exon_variant	0.55	linezolid	Uncertain significance
rrl	1474827	n.1170C>T	non_coding_transcript_exon_variant	0.55	capreomycin	Uncertain significance
rrl	1474827	n.1170C>T	non_coding_transcript_exon_variant	0.55	linezolid	Uncertain significance
rrl	1474830	n.1173A>T	non_coding_transcript_exon_variant	0.55	capreomycin	Uncertain significance
rrl	1474830	n.1173A>T	non_coding_transcript_exon_variant	0.55	linezolid	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.67	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.67	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.58	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.58	linezolid	Uncertain significance
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.32	capreomycin
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.32	linezolid
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.63	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.63	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.3	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.3	linezolid
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.36	capreomycin	Uncertain significance
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.36	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.65	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.65	linezolid	Uncertain significance
rrl	1476429	n.2772A>T	non_coding_transcript_exon_variant	0.35	capreomycin	Uncertain significance
rrl	1476429	n.2772A>T	non_coding_transcript_exon_variant	0.35	linezolid
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.29	capreomycin
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.29	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.89	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.88	capreomycin	Not assoc w R
rrl	1476481	n.2824T>C	non_coding_transcript_exon_variant	0.88	linezolid	Uncertain significance