Full information on isolate Ag08_2020 (id:1054)
Provenance/primary metadata
- id
- 1054
- isolate
- Ag08_2020
- aliases
- Ag8_Sejroe; Sponselee
- biosample
- P1
- clade
- P1
- species
- borgpetersenii
- serogroup
- Sejroe
- serovar
- unknown
- sequencing year
- 2020
- world region
- Western Europe
- country
- France
- host
- unknown
- sample type
- culture
- source lab
- CNR_leptospirose
- comments
- 2020 contrôle annuel antigènes
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 16 updates show details
- date entered
- 2020-04-02
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 387
- total length
- 3,896,757 bp
- max length
- 63,357 bp
- mean length
- 10,070 bp
- N50
- 20,161
- L50
- 63
- N90
- 5,619
- L90
- 191
- N95
- 3,811
- L95
- 232
- %GC
- 40.23
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,135
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 529 | 97 | |
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 72 (43 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 69 (43 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 74 (43 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 69 (43 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 65 (43 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 72 (43 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 69 (43 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 74 (43 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 69 (43 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 65 (43 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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