TB-Profiler result

Run: e5f47056-9cba-4aa8-b8d5-8c9264faad4b
Summary

Run ID: e5f47056-9cba-4aa8-b8d5-8c9264faad4b

Sample name:

Date: 15-03-2023 12:39:25

Number of reads: 738749

Percentage reads mapped: 96.9

Median coverage: 18

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: RR-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.Ser450Leu Assoc w R
isoniazid
ethambutol
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin 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 9730 p.Asp810Val missense_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 490645 c.-138T>C upstream_gene_variant 0.11 delamanid
ccsA 619831 c.-60T>G upstream_gene_variant 0.29 capreomycin
amikacin
rpoB 761304 p.Val500Leu missense_variant 0.25 rifampicin
rpoB 761307 p.Asn501Asp missense_variant 0.27 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 765750 p.Pro794Leu missense_variant 0.12 rifampicin
rpoC 766642 p.His1091Gln missense_variant 0.64 rifampicin
mmpL5 779061 c.-581G>A upstream_gene_variant 0.13 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1305170 p.Gln747Leu missense_variant 0.2 delamanid
Rv1258c 1406787 p.Ile185Asn missense_variant 0.13 streptomycin
pyrazinamide
isoniazid
fabG1 1673346 c.-94C>G upstream_gene_variant 0.28 ethionamide
isoniazid
fabG1 1673349 c.-91G>C upstream_gene_variant 0.28 ethionamide
isoniazid
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14 ethionamide
isoniazid
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14 ethionamide
isoniazid
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14 ethionamide
isoniazid
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
ribD 2987132 p.Met98Ile missense_variant 0.14 para-aminosalicylic_acid
ribD 2987137 p.Val100Gly missense_variant 0.15 para-aminosalicylic_acid
ribD 2987143 p.Gln102Arg missense_variant 0.14 para-aminosalicylic_acid
Rv2752c 3066237 c.-47_-46delCCinsTT upstream_gene_variant 1.0 rifampicin
isoniazid
thyX 3067674 p.His91Leu missense_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiB 3642101 c.567C>T synonymous_variant 0.13 delamanid
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.66 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.3 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.9 capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338440 c.81_82insC frameshift_variant 1.0 streptomycin
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance