TB-Profiler result

Run: SRR28393400
Summary

Run ID: SRR28393400

Sample name:

Date: 2024-10-05T06:48:36.624969

Number of reads: 3128083

Percentage reads mapped: 99.57

Median coverage: 89.0

Strain: lineage2.2.1.1;lineage4.3.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.42
lineage2 East-Asian RD105 0.59
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.55
lineage2.2 East-Asian (Beijing) RD105;RD207 0.62
lineage4 Euro-American None 0.46
lineage4.3.3 Euro-American (LAM) RD115 0.42
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.45
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu85Arg Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 0.59 isoniazid Assoc w R High-level resistance
pncA 2288988 p.Leu85Arg missense_variant 0.14 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.13 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.39 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
fgd1 491742 c.960T>C synonymous_variant 0.56 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.45 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.51 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.64 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.64 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.61 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.48 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.46 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.45 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.6 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.56 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.51 pyrazinamide Not assoc w R - Interim
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 2154724 p.Arg463Leu missense_variant 0.63 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.66 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.36 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.48 kanamycin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783921 p.Gly41Glu missense_variant 0.49 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2784034 c.9G>A synonymous_variant 0.45 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.36 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.59 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641643 p.Ala37Ser missense_variant 0.53 pretomanid
delamanid
clofazimine
clpC1 4038287 c.2418C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
glpK 4139024 c.732G>A synonymous_variant 0.58 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242182 p.Ala774Ser missense_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.64 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.56 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.55 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.53 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.55 streptomycin Not assoc w R
gid 4407973 p.Val77Gly missense_variant 0.44 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.38 streptomycin Not assoc w R