TB-Profiler result

Run: ERR4827957
Summary

Run ID: ERR4827957

Sample name:

Date: 2024-03-26T20:48:12.883132

Number of reads: 4118374

Percentage reads mapped: 99.5

Median coverage: 111.5

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.13
lineage2 East-Asian RD105 0.89
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.87
lineage2.2 East-Asian (Beijing) RD105;RD207 0.9
lineage4 Euro-American None 0.13
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 rpsL p.Lys43Arg 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
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8042 c.741C>T synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.87 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.87 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619815 c.-76G>C upstream_gene_variant 0.86 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.92 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.89 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.86 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.82 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.87 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776371 p.Gly704Cys missense_variant 0.14 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.9 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.93 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.89 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674026 c.-176A>C upstream_gene_variant 0.9 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.84 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 0.9 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.84 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.11 pyrazinamide
PPE35 2170521 p.Trp31* stop_gained 0.17 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.14 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
ald 3086788 c.-32T>C upstream_gene_variant 0.88 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.85 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.85 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.16 pyrazinamide Not assoc w R
glpK 4139760 c.-5A>G upstream_gene_variant 0.87 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.92 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.92 ethambutol Not assoc w R
ubiA 4269871 c.-38G>A upstream_gene_variant 0.88 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.91 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.87 streptomycin Not assoc w R