Full information on isolate SOFTIC (id:166)
Provenance/primary metadata
- id
- 166
- isolate
- SOFTIC
- clade
- P1
- species
- interrogans
- serogroup
- Pomona
- serovar
- Pomona
- isolation year
- 1984
- sequencing year
- 2022
- passage
- 456
- world region
- Eastern Europe
- country
- Croatia
- city
- Zagreb
- host
- human
- 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
- 2024-04-25
Sequence bin
- contigs
- 197
- total length
- 4,536,201 bp
- max length
- 211,365 bp
- mean length
- 23,027 bp
- N50
- 41,667
- L50
- 31
- N90
- 14,633
- L90
- 102
- N95
- 8,344
- L95
- 122
- %GC
- 34.95
- 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-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
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