TB-Profiler result

Run: ERR4828397
Summary

Run ID: ERR4828397

Sample name:

Date: 2024-04-15T04:40:02.897672

Number of reads: 1794448

Percentage reads mapped: 99.59

Median coverage: 48.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.3
lineage2 East-Asian RD105 0.68
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.67
lineage4 Euro-American None 0.33
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
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.62 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.73 isoniazid Assoc w R High-level resistance
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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9524 c.2223G>A synonymous_variant 0.58 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.76 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620029 c.139C>T synonymous_variant 0.3 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.8 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.59 ethionamide Uncertain significance
rpoB 759724 c.-83A>G upstream_gene_variant 0.5 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.73 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.74 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800513 c.-296G>A upstream_gene_variant 0.27 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.59 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 0.98 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.72 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.68 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.45 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.71 cycloserine
Rv3083 3449945 p.Gly481Asp missense_variant 0.74 ethionamide Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.69 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.59 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.63 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 0.38 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.47 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242775 c.2913G>A synonymous_variant 0.3 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.67 ethambutol Not assoc w R
embA 4246449 p.Val1073Ile missense_variant 0.32 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.69 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.75 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.65 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.52 streptomycin Not assoc w R