TB-Profiler

TB-Profiler result

Run: SRR7061280

Summary

Run ID: SRR7061280

Sample name:

Date: 2024-04-16T06:24:37.275249

Number of reads: 42773520

Percentage reads mapped: 99.12

Median coverage: 307.0

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	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473336	n.1491T>G	non_coding_transcript_exon_variant	0.27	streptomycin
					kanamycin
					capreomycin
					amikacin
rrs	1473352	n.1507C>T	non_coding_transcript_exon_variant	0.13	streptomycin	Uncertain significance
					kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Not assoc w R
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.1	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.1	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.16	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.16	linezolid	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.22	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.22	linezolid	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.15	capreomycin	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.15	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.23	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.23	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.15	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.15	linezolid	Uncertain significance
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.15	capreomycin
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.15	linezolid
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.15	capreomycin
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.15	linezolid
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.15	capreomycin
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.15	linezolid
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.15	capreomycin
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.15	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.13	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.13	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.25	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.25	linezolid	Uncertain significance
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.12	capreomycin	Not assoc w R
rrl	1476506	n.2849T>C	non_coding_transcript_exon_variant	0.12	linezolid	Uncertain significance