TB-Profiler result

Run: ERR10748234
Summary

Run ID: ERR10748234

Sample name:

Date: 2024-04-16T11:53:33.192536

Number of reads: 689304

Percentage reads mapped: 99.76

Median coverage: 34.0

Strain: lineage2.2.1;lineage4.1.1.2

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.1.2 Euro-American (X-type) None 0.7
lineage2 East-Asian RD105 0.27
lineage4.1 Euro-American None 0.72
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.36
lineage2.2 East-Asian (Beijing) RD105;RD207 0.31
lineage4 Euro-American None 0.73
lineage4.1.1 Euro-American (X-type) None 0.77
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
ethambutol embB p.Met306Ile Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.33 ethambutol 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
mshA 575907 p.Ala187Val missense_variant 0.34 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.31 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657142 p.Arg110His missense_variant 0.26 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.7 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.57 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.69 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.32 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 0.22 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 0.41 pyrazinamide Not assoc w R - Interim
tsnR 1854268 p.Ile221Met missense_variant 0.69 linezolid Uncertain significance
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 2155296 c.816C>T synonymous_variant 0.81 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.31 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 2783725 c.318C>T synonymous_variant 0.66 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449787 c.1284C>T synonymous_variant 0.76 ethionamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626305 c.309C>T synonymous_variant 0.76 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840597 p.Met275Thr missense_variant 0.32 cycloserine
clpC1 4039676 c.1029G>A synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.83 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.24 ethambutol Not assoc w R
embA 4243833 p.Ala201Thr missense_variant 0.71 ethambutol Not assoc w R
embB 4246930 p.Gln139His missense_variant 0.72 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.58 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.26 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 0.32 streptomycin Not assoc w R