Full information on isolate 325_IZSLER (id:1587)
Provenance/primary metadata
- id
- 1587
- isolate
- 325_IZSLER
- clade
- P1
- species
- interrogans
- serogroup
- Australis
- serovar
- Muenchen
- isolation year
- 2010
- sequencing year
- 2023
- world region
- Western Europe
- country
- Italy
- host
- wild boar
- sample type
- kidney
- source lab
- IZSLER
- sender
- Bertasio Cristina, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia (Italy)
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 7 updates show details
- date entered
- 2024-01-15
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 239
- total length
- 4,629,697 bp
- max length
- 257,698 bp
- mean length
- 19,372 bp
- N50
- 69,125
- L50
- 19
- N90
- 17,826
- L90
- 69
- N95
- 11,248
- L95
- 85
- %GC
- 34.97
- Ns
- 0
- gaps
- 0
- loci tagged
- 620
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 | 543 | 99 | |
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 | 69 (12 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 12 (16 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 60 (6 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 57 (16 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 11 (16 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 69 (12 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 12 (16 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 60 (6 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 57 (16 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 11 (16 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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