TB-Profiler result

Run: ERR10748565
Summary

Run ID: ERR10748565

Sample name:

Date: 2024-04-16T01:55:28.957250

Number of reads: 2791302

Percentage reads mapped: 99.22

Median coverage: 88.0

Strain: lineage2.2.1.1;lineage4.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.9
lineage4.1.2 Euro-American None 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.87
lineage2.2 East-Asian (Beijing) RD105;RD207 0.92
lineage4 Euro-American None 0.12
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.46
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Thr76Pro Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethR p.Ala95Thr Uncertain significance Mutation from literature
p.Phe110Leu Uncertain significance Mutation from literature
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 761155 p.Ser450Leu missense_variant 0.52 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.38 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
pncA 2289016 p.Thr76Pro missense_variant 0.29 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol Assoc w R
ethR 4327831 p.Ala95Thr missense_variant 0.3 ethionamide Uncertain significance Mutation from literature
ethR 4327876 p.Phe110Leu missense_variant 0.12 ethionamide Uncertain significance Mutation from literature
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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.12 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.89 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.85 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575980 p.Asp211Glu missense_variant 0.12 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.85 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.93 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.93 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 763555 c.186C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 766699 p.Gln1110His missense_variant 0.37 rifampicin Uncertain significance
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 0.93 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.94 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 778979 c.-74G>T upstream_gene_variant 0.34 clofazimine Uncertain significance
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.91 clofazimine
bedaquiline
rpsL 781301 c.-259C>T upstream_gene_variant 0.51 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800889 c.81C>A synonymous_variant 0.13 linezolid Not assoc w R - Interim
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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.84 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.88 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
bacA 2064271 p.Trp153Ser missense_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.93 isoniazid Not assoc w R
katG 2155724 p.Ala130Thr missense_variant 0.42 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.95 pyrazinamide Not assoc w R
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.49 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.47 amikacin Not assoc w R
kanamycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.84 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 0.91 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.89 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.44 ethambutol Not assoc w R
aftB 4267091 c.1746C>A synonymous_variant 0.12 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.88 ethambutol Not assoc w R
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 0.9 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.87 streptomycin Not assoc w R