TB-Profiler result

Run: ERR2747617
Summary

Run ID: ERR2747617

Sample name:

Date: 2024-10-04T21:42:49.207887

Number of reads: 375248

Percentage reads mapped: 10.98

Median coverage: 6.0

Strain: La1.8.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.8 M.bovis None 1.0
La1.8.1 M.bovis None 1.0
La1 M.bovis 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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473165 n.1320C>T non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473193 n.1348G>T non_coding_transcript_exon_variant 0.8 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473200 n.1355A>C non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473204 n.1359C>A non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476354 n.2697A>G non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476388 n.2731T>C non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476451 n.2794C>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide Uncertain significance
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin