TB-Profiler result

Run: ERR221659
Summary

Run ID: ERR221659

Sample name:

Date: 2024-10-04T14:30:48.598478

Number of reads: 8742963

Percentage reads mapped: 99.66

Median coverage: 197.0

Strain: lineage2.2.1;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.74
lineage2 East-Asian RD105 0.3
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.29
lineage2.2 East-Asian (Beijing) RD105;RD207 0.31
lineage4 Euro-American None 0.74
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.7
lineage4.3.4 Euro-American (LAM) RD174 0.71
lineage4.3.4.2 Euro-American (LAM) RD174 0.72
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
gyrB 6140 p.Val301Leu missense_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 0.28 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.32 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.24 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.24 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.75 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.23 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.28 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.28 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.26 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
ndh 2103226 c.-184C>G upstream_gene_variant 0.27 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 0.27 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.31 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2746859 p.Ala247Val missense_variant 0.75 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.71 para-aminosalicylic_acid
ald 3086739 c.-81G>A upstream_gene_variant 0.28 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.65 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.25 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.69 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.76 pyrazinamide 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 0.27 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.26 ethambutol Not assoc w R
ubiA 4269920 c.-87G>A upstream_gene_variant 0.74 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.24 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.32 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.7 streptomycin Not assoc w R