Full information on isolate VARDARAC (id:164)
Provenance/primary metadata
- id
- 164
- isolate
- VARDARAC
- clade
- P1
- species
- interrogans
- serogroup
- Pomona
- serovar
- Pomona
- isolation year
- 1976
- sequencing year
- 2022
- passage
- 520
- world region
- Eastern Europe
- country
- Croatia
- city
- Baranja
- host
- cat
- 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
- 9 updates show details
- date entered
- 2022-11-17
- datestamp
- 2024-04-17
Sequence bin
- method
- Illumina
- contigs
- 206
- total length
- 4,603,534 bp
- max length
- 184,134 bp
- mean length
- 22,348 bp
- N50
- 43,069
- L50
- 32
- N90
- 13,815
- L90
- 106
- N95
- 8,551
- L95
- 126
- %GC
- 34.95
- Ns
- 0
- gaps
- 0
- loci tagged
- 605
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 | 5 (74 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 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-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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