TB-Profiler result

Run: ERR4810570
Summary

Run ID: ERR4810570

Sample name:

Date: 2024-04-16T09:52:22.971206

Number of reads: 6178088

Percentage reads mapped: 98.99

Median coverage: 185.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.52
lineage2 East-Asian RD105 0.48
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.5
lineage2.2 East-Asian (Beijing) RD105;RD207 0.5
lineage4 Euro-American None 0.51
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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.57 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
Rv0010c 13569 c.-11C>T upstream_gene_variant 0.47 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.55 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620029 c.139C>T synonymous_variant 0.56 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.52 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.43 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.52 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 0.54 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776312 p.Glu723Asp missense_variant 0.51 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 778243 p.Lys80Gln missense_variant 0.51 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.51 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801426 c.618C>T synonymous_variant 0.54 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.5 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302927 c.-4C>T upstream_gene_variant 0.49 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.43 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674043 c.-159G>T upstream_gene_variant 0.51 ethionamide
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.47 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 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.47 pyrazinamide Not assoc w R
PPE35 2169242 c.1370delG frameshift_variant 0.55 pyrazinamide Uncertain significance
PPE35 2170030 c.549_582delGGCCGTGGTGACCGCGCTCACCACGGCCGTGGGC frameshift_variant 0.44 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.53 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
Rv2477c 2782403 p.Pro547Leu missense_variant 0.46 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2752c 3065129 c.1063C>T synonymous_variant 0.48 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyX 3067975 c.-30C>T upstream_gene_variant 0.54 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.54 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.42 pyrazinamide Not assoc w R - Interim
lpqB 3624398 c.513C>T synonymous_variant 0.54 bedaquiline Not assoc w R - Interim
rifampicin 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 0.45 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878575 c.-68C>T upstream_gene_variant 0.42 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.55 pyrazinamide Not assoc w R
embC 4239046 c.-817T>G upstream_gene_variant 0.47 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.48 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.52 ethambutol Not assoc w R
aftB 4268495 c.342G>C synonymous_variant 0.53 ethambutol Not assoc w R - Interim
ethA 4326676 p.Ser266Arg missense_variant 0.49 ethionamide Uncertain significance
ethA 4326937 c.537C>T synonymous_variant 0.51 ethionamide Not assoc w R - Interim
whiB6 4338359 p.Ala55Pro missense_variant 0.4 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.51 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.45 streptomycin Not assoc w R