TB-Profiler result

Run: ada6cbaa-b3a9-45f5-9a93-d5bb12630ad4
Summary

Run ID: ada6cbaa-b3a9-45f5-9a93-d5bb12630ad4

Sample name:

Date: 26-12-2023 03:41:20

Number of reads: 746020

Percentage reads mapped: 99.39

Median coverage: 27

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
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
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
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
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
rpoB 759956 c.150C>A synonymous_variant 0.1 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 766361 p.Val998Met missense_variant 0.12 rifampicin
rpoC 766579 c.3210C>T synonymous_variant 0.1 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 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 778622 p.Thr95Met missense_variant 0.11 clofazimine
bedaquiline
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
fbiC 1303999 p.Val357Ile missense_variant 0.12 delamanid
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
ndh 2101681 c.1362C>A synonymous_variant 0.11 ethionamide
isoniazid
ndh 2102345 p.Ala233Gly missense_variant 0.11 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170411 p.Ala68Ser missense_variant 0.11 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
folC 2747420 p.Pro60Leu missense_variant 0.11 para-aminosalicylic_acid
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0 rifampicin
isoniazid
Rv2752c 3067074 c.-883C>T upstream_gene_variant 0.11 rifampicin
isoniazid
thyX 3067245 p.Thr234Ile missense_variant 0.15 para-aminosalicylic_acid
thyX 3067264 p.Ala228Thr missense_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448437 c.-67C>T upstream_gene_variant 0.11 ethionamide
Rv3083 3449172 c.669C>T synonymous_variant 0.13 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
fbiB 3642463 p.Leu310Pro missense_variant 0.13 delamanid
rpoA 3878061 c.447G>T synonymous_variant 0.12 rifampicin
clpC1 4038379 p.Thr776Ser missense_variant 0.12 pyrazinamide
clpC1 4040307 p.Arg133Leu missense_variant 0.14 pyrazinamide
clpC1 4040324 c.381G>T synonymous_variant 0.15 pyrazinamide
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4242652 c.-581C>A upstream_gene_variant 0.14 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
embA 4244194 p.Gly321Val missense_variant 0.12 ethambutol
embA 4244871 p.Gly547Cys missense_variant 0.17 ethambutol
embB 4247163 p.Leu217Pro missense_variant 0.11 ethambutol
embB 4247974 c.1461C>A synonymous_variant 0.11 ethambutol
embB 4248692 p.Val727Met missense_variant 0.1 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
aftB 4268625 p.Gly71Asp missense_variant 0.12 capreomycin
amikacin
ubiA 4268947 p.Gly296Val missense_variant 0.17 ethambutol
ubiA 4269625 p.Tyr70Cys missense_variant 0.11 ethambutol
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
gid 4408342 c.-140C>T upstream_gene_variant 0.1 streptomycin