TB-Profiler result

Run: ERR2706940
Summary

Run ID: ERR2706940

Sample name:

Date: 2024-10-03T21:55:04.612051

Number of reads: 5298206

Percentage reads mapped: 99.73

Median coverage: 160.0

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.Ile491Phe Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
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
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol 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
gyrB 6379 c.1140C>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 574906 c.-442G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
hadA 732110 p.Cys61Gly missense_variant 1.0 isoniazid Uncertain significance
rplC 800178 c.-631C>T upstream_gene_variant 1.0 linezolid
rplC 801355 p.His183Tyr missense_variant 1.0 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154322 p.Tyr597Ser missense_variant 1.0 isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
PPE35 2170036 p.Val193Met missense_variant 1.0 pyrazinamide Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.34 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R