TB-Profiler result

Run: ERR1199119
Summary

Run ID: ERR1199119

Sample name:

Date: 2025-05-03T20:25:08.237411

Number of reads: 5099737

Percentage reads mapped: 99.74

Median coverage: 160.0

Strain: lineage4.6.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.93
lineage4 Euro-American None 1.0
lineage4.6.1 Euro-American (Uganda) RD724 0.83
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
gyrA 7539 p.Thr80Ala missense_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8717 c.1416C>T synonymous_variant 0.94 levofloxacin Not assoc w R - Interim
moxifloxacin Uncertain significance
gyrA 8774 c.1473C>A synonymous_variant 0.92 levofloxacin Not assoc w R - Interim
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417040 p.Leu103Arg missense_variant 0.93 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2221767 p.His466Gln missense_variant 0.94 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2681 2996876 c.138A>C synonymous_variant 0.92 capreomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 0.94 amikacin Uncertain significance
kanamycin Not assoc w R
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139183 c.570_572dupGGG disruptive_inframe_insertion 0.77 ethambutol Uncertain significance
isoniazid Not assoc w R
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
streptomycin Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 0.95 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Not assoc w R
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338391 p.Thr44Ile missense_variant 0.94 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407555 c.648A>G synonymous_variant 0.89 streptomycin Not assoc w R - Interim