TB-Profiler result

Run: SRR10808922
Summary

Run ID: SRR10808922

Sample name:

Date: 2024-04-15T02:37:52.681113

Number of reads: 3103464

Percentage reads mapped: 99.59

Median coverage: 101.0

Strain: lineage2.2.1;lineage4.4.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.8
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 0.24
lineage4.4 Euro-American None 0.2
lineage4.4.2 Euro-American None 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
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
inhA 1673423 c.-779G>T upstream_gene_variant 0.16 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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 7017 p.Ala593Val missense_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 491742 c.960T>C synonymous_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.83 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.73 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.77 ethionamide Uncertain significance
rpoB 759485 c.-321delC upstream_gene_variant 0.16 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.74 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 0.81 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.73 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83 clofazimine
bedaquiline
rpsL 781326 c.-233delG upstream_gene_variant 0.17 streptomycin Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.81 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 0.83 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 0.85 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 0.87 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2168602 c.2010delC frameshift_variant 0.1 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ribD 2987049 p.Phe71Val missense_variant 0.79 para-aminosalicylic_acid
Rv2752c 3066099 p.Met31Ile missense_variant 0.21 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.79 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625342 c.1272C>G synonymous_variant 0.29 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.79 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640321 c.-222T>G upstream_gene_variant 0.76 clofazimine
pretomanid
delamanid
embC 4238963 c.-900C>T upstream_gene_variant 0.14 ethambutol 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 0.74 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.24 ethambutol Not assoc w R
embB 4249495 p.Phe994Leu missense_variant 0.84 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.69 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.17 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.21 ethambutol Not assoc w R
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 0.68 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338594 c.-75delG upstream_gene_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 0.68 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338594 c.-75delG upstream_gene_variant 0.32 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 0.78 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.87 streptomycin Not assoc w R