TB-Profiler result

Run: 7239a640-5882-4aa5-8696-9e968c5ecac1
Summary

Run ID: 7239a640-5882-4aa5-8696-9e968c5ecac1

Sample name:

Date: 15-02-2023 08:37:53

Number of reads: 988999

Percentage reads mapped: 96.51

Median coverage: 25

Strain: lineage3.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.99
lineage3.1 East-African-Indian RD750 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 0.83 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
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 576108 p.Ala254Gly missense_variant 0.17 ethionamide Uncertain significance
isoniazid
mshA 576113 p.Arg256Gly missense_variant 0.26 ethionamide
isoniazid
mshA 576613 c.1266A>C synonymous_variant 0.18 ethionamide
isoniazid
rpoC 762434 c.-936T>G upstream_gene_variant 0.87 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 764918 p.Val517Leu missense_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776182 p.Asp767Asn missense_variant 0.12 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rpsL 781502 c.-58G>A upstream_gene_variant 0.12 streptomycin
rpsL 781507 c.-53G>T upstream_gene_variant 0.12 streptomycin
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.12 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407243 p.Leu33Gln missense_variant 0.14 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
fabG1 1674124 p.Ala229Thr missense_variant 0.12 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2101861 c.1182G>A synonymous_variant 0.77 ethionamide
isoniazid
ndh 2102242 c.801G>C synonymous_variant 0.11 ethionamide
isoniazid
ndh 2102817 p.Leu76Val missense_variant 0.17 ethionamide
isoniazid
katG 2154452 p.Lys554Glu missense_variant 0.15 isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2170301 p.Met104Ile missense_variant 0.11 pyrazinamide
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.9 isoniazid Uncertain significance
ahpC 2726117 c.-76T>A upstream_gene_variant 0.9 isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fbiB 3641551 p.His6Arg missense_variant 0.15 delamanid
fbiB 3642386 c.852C>T synonymous_variant 0.1 delamanid
clpC1 4040009 c.696C>T synonymous_variant 0.12 pyrazinamide
clpC1 4040015 c.690G>A synonymous_variant 0.14 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.14 pyrazinamide
clpC1 4040024 c.681A>G synonymous_variant 0.14 pyrazinamide
clpC1 4040027 c.678C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040042 c.663C>T synonymous_variant 0.14 pyrazinamide
clpC1 4040057 c.648C>T synonymous_variant 0.13 pyrazinamide
clpC1 4040060 c.645C>T synonymous_variant 0.13 pyrazinamide
clpC1 4040066 c.639G>T synonymous_variant 0.11 pyrazinamide
clpC1 4040069 c.636G>C synonymous_variant 0.11 pyrazinamide
clpC1 4040084 c.621C>T synonymous_variant 0.17 pyrazinamide
clpC1 4040087 c.618G>C synonymous_variant 0.17 pyrazinamide
clpC1 4040090 c.615T>C synonymous_variant 0.17 pyrazinamide
clpC1 4040096 c.609G>C synonymous_variant 0.17 pyrazinamide
clpC1 4040108 c.597G>C synonymous_variant 0.17 pyrazinamide
clpC1 4040111 c.594G>A synonymous_variant 0.18 pyrazinamide
clpC1 4040114 p.Ile197Met missense_variant 0.18 pyrazinamide
clpC1 4040117 c.588A>G synonymous_variant 0.18 pyrazinamide
clpC1 4040123 p.Glu194His missense_variant 0.17 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 0.97 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embB 4248324 p.Ala604Gly missense_variant 0.25 ethambutol
ethA 4326756 p.Trp240Arg missense_variant 0.96 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