TB-Profiler

TB-Profiler result

Run: SRR13861402

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: SRR13861402

Sample name:

Date: 2024-10-05T04:58:30.828454

Number of reads: 230091

Percentage reads mapped: 7.68

Median coverage: 7.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON

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	Comment
rifampicin
isoniazid
ethambutol	embC	p.Tyr296His	Mutation from literature
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
embC	4240748	p.Tyr296His	missense_variant	1.0	ethambutol		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	760225	p.Glu140Ala	missense_variant	1.0	rifampicin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.83	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.83	linezolid
rrl	1476356	n.2699C>A	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1476356	n.2699C>A	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.9	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.9	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476383	n.2726T>G	non_coding_transcript_exon_variant	0.92	capreomycin
rrl	1476383	n.2726T>G	non_coding_transcript_exon_variant	0.92	linezolid
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.9	capreomycin
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.9	linezolid
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.92	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.92	linezolid
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.92	capreomycin
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.92	linezolid
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.92	capreomycin
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.92	linezolid
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.9	capreomycin
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.9	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.89	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.89	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.88	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.88	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.62	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.62	linezolid	Uncertain significance
fbiA	3640219	c.-324C>T	upstream_gene_variant	1.0	pretomanid
					delamanid
					clofazimine
ethR	4328162	p.His205Pro	missense_variant	1.0	ethionamide