Full information on isolate R 25/75 (id:34)
Provenance/primary metadata
- id
- 34
- isolate
- R 25/75
- clade
- P1
- species
- interrogans
- serogroup
- Pomona
- serovar
- Kennewicki
- isolation year
- 1977
- sequencing year
- 2022
- passage
- 450
- world region
- Eastern Europe
- country
- Croatia
- city
- Durdenovac
- host
- hare
- sample type
- Blood
- source lab
- LEPTOlab
- sender
- Iva Zečević, Faculty of Veterinary Medicine, University of Zagreb
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 10 updates show details
- date entered
- 2022-11-17
- datestamp
- 2024-04-17
Sequence bin
- contigs
- 171
- total length
- 4,539,795 bp
- max length
- 223,114 bp
- mean length
- 26,549 bp
- N50
- 54,949
- L50
- 24
- N90
- 15,622
- L90
- 82
- N95
- 9,746
- L95
- 100
- %GC
- 34.93
- Ns
- 0
- gaps
- 0
- loci tagged
- 606
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 | 544 | 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 | 5 (74 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 5 (31 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 179 (7 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 5 (40 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 5 (40 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 5 (40 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 5 (43 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 5 (31 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (45 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (77 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 5 (74 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 5 (31 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 179 (7 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 5 (40 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 5 (40 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 5 (40 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 5 (43 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 5 (31 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (45 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (77 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
Schemes and loci
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