TB-Profiler result

Run: ERR4812105
Summary

Run ID: ERR4812105

Sample name:

Date: 2024-04-15T16:23:05.010102

Number of reads: 6074914

Percentage reads mapped: 99.47

Median coverage: 231.5

Strain: lineage2.2.1.1;lineage4.3.4.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.67
lineage2 East-Asian RD105 0.34
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.32
lineage2.2 East-Asian (Beijing) RD105;RD207 0.33
lineage4.3.4.1 Euro-American (LAM) RD174 0.67
lineage4.3.4 Euro-American (LAM) RD174 0.69
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.32
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.180delA 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
katG 2155168 p.Ser315Thr missense_variant 0.65 isoniazid Assoc w R High-level resistance
gid 4408022 c.180delA frameshift_variant 0.59 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 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 0.32 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.31 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.34 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.34 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.63 rifampicin Not assoc w R
rpoC 765590 p.Arg741Ser missense_variant 0.7 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 0.36 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.37 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36 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 0.33 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.66 pyrazinamide Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29 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 0.37 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>C synonymous_variant 0.64 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 0.36 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.35 pyrazinamide Not assoc w R
Rv1979c 2223123 c.42G>A synonymous_variant 0.62 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
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 0.34 amikacin Not assoc w R
kanamycin Not assoc w R
Rv2477c 2784034 c.9G>A synonymous_variant 0.28 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.62 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2681 2998047 p.Gly437Ser missense_variant 0.12 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.64 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.72 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.3 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 0.39 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641643 p.Ala37Ser missense_variant 0.33 clofazimine
pretomanid
delamanid
clpC1 4038287 c.2418C>T synonymous_variant 0.7 pyrazinamide Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.49 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.3 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.2 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 0.3 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.39 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.62 streptomycin Not assoc w R