TB-Profiler result

Run: ERR2184309
Summary

Run ID: ERR2184309

Sample name:

Date: 2024-04-15T13:33:38.974543

Number of reads: 3077070

Percentage reads mapped: 99.79

Median coverage: 106.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: MDR-TB

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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 rpoB p.Val170Phe Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.754_755dupGC Assoc w R
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
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4249583 p.Asp1024Asn missense_variant 0.11 ethambutol Uncertain significance Mutation from literature
ethA 4326718 c.754_755dupGC frameshift_variant 0.64 ethionamide Assoc w R
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
nusG 734935 p.Val228Leu missense_variant 0.28 rifampicin
rpoB 762685 p.Ala960Glu missense_variant 1.0 rifampicin Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 1.0 rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv2680 2996096 c.-9G>A upstream_gene_variant 0.53 capreomycin
mtrA 3627478 c.-129G>C upstream_gene_variant 0.99 bedaquiline Uncertain significance
rifampicin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
gid 4407758 p.Ser149Arg missense_variant 1.0 streptomycin Uncertain significance