TB-Profiler result

Run: afa29974-326a-446a-87a9-7aeb1a5e446d
Summary

Run ID: afa29974-326a-446a-87a9-7aeb1a5e446d

Sample name:

Date: 08-05-2024 02:27:19

Number of reads: 5030339

Percentage reads mapped: 89.66

Median coverage: 90

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Asn Assoc w R
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rpsL p.Lys43Arg Assoc w R
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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 761161 p.Leu452Pro missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.96 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 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
rpoC 762836 c.-534C>G upstream_gene_variant 0.26 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.99 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776517 p.Met655Thr missense_variant 0.99 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169320 p.Leu431Phe missense_variant 0.18 pyrazinamide
PPE35 2169866 c.747G>C synonymous_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pepQ 2859381 c.1038C>G synonymous_variant 0.23 clofazimine
bedaquiline
ribD 2987091 p.Val85Met missense_variant 0.99 para-aminosalicylic_acid
Rv2752c 3064552 p.Arg547Pro missense_variant 0.23 rifampicin
isoniazid
thyA 3073806 c.666C>G synonymous_variant 0.16 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4038857 c.1848C>A synonymous_variant 0.14 pyrazinamide
clpC1 4039932 p.Gly258Val missense_variant 0.26 pyrazinamide
embC 4239842 c.-21C>A upstream_gene_variant 0.13 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242822 p.Val987Gly missense_variant 0.33 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
ubiA 4269529 p.Ala102Gly missense_variant 0.26 ethambutol
ethA 4326676 p.Ser266Arg missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance