TB-Profiler result

Run: ERR2600525
Summary

Run ID: ERR2600525

Sample name:

Date: 2024-04-15T18:38:27.742757

Number of reads: 1152993

Percentage reads mapped: 99.11

Median coverage: 24.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.06
lineage4.1.2 Euro-American None 0.1
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.09
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.89
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13680 c.-122G>A upstream_gene_variant 0.76 isoniazid Uncertain significance
rpoC 765691 c.2322G>T synonymous_variant 0.39 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.26 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.9 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854329 p.Val242Phe missense_variant 0.9 linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.8 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.8 capreomycin
ddn 3986815 c.-29G>C upstream_gene_variant 0.89 delamanid
pretomanid
panD 4044824 c.-543C>T upstream_gene_variant 0.3 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.79 capreomycin
amikacin
kanamycin