TB-Profiler result

Run: ERR11465076
Summary

Run ID: ERR11465076

Sample name:

Date: 2024-10-05T09:21:00.380120

Number of reads: 6719674

Percentage reads mapped: 99.66

Median coverage: 192.0

Strain: lineage2.2.1;lineage4.4.1.1

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 0.49
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.5
lineage2.2 East-Asian (Beijing) RD105;RD207 0.5
lineage4.4.1 Euro-American (S-type) None 0.5
lineage4 Euro-American None 0.53
lineage4.4.1.1 Euro-American None 0.52
lineage4.4 Euro-American None 0.5
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
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
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 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 9138 p.Gln613Glu missense_variant 0.5 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 0.6 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.5 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.51 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 0.52 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777416 c.1065G>T synonymous_variant 0.47 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.41 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 0.48 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 0.49 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 0.52 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
tlyA 1918142 p.His68Arg missense_variant 0.47 capreomycin Uncertain significance
tlyA 1918283 p.Tyr115Cys missense_variant 0.55 capreomycin
ndh 2102990 p.Val18Ala missense_variant 0.49 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.4 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.4 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.44 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.61 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
Rv2752c 3065453 p.Gln247* stop_gained 0.51 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.51 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.53 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.58 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.44 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.58 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640879 c.337C>T synonymous_variant 0.49 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
glpK 4139535 p.Val74Ala missense_variant 0.78 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4238963 c.-900C>T upstream_gene_variant 0.46 ethambutol Not assoc w R
embC 4241053 c.1191G>A synonymous_variant 0.53 ethambutol
embC 4241306 p.Val482Ile missense_variant 0.62 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.59 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.42 ethambutol Not assoc w R
ethA 4326474 p.Pro334Ala missense_variant 0.55 ethionamide Uncertain significance
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 1.0 kanamycin
capreomycin
amikacin
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