Full information on isolate RR-KS-YR03-1 (id:1789)
Provenance/primary metadata
- id
- 1789
- isolate
- RR-KS-YR03-1
- biosample
- SAMD00754719
- clade
- P1
- species
- borgpetersenii
- serogroup
- Javanica
- serovar
- not examined
- isolation year
- 2003
- world region
- Eastern Asia
- country
- Japan
- host
- rat
- sample type
- kidney
- source lab
- NIID
- sender
- Nobuo Koizumi, National institute of infectious diseases, Japan
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 5 updates show details
- date entered
- 2024-03-28
- datestamp
- 2024-04-17
Sequence bin
- contigs
- 61
- total length
- 3,883,759 bp
- max length
- 396,938 bp
- mean length
- 63,669 bp
- N50
- 152,251
- L50
- 8
- N90
- 38,207
- L90
- 24
- N95
- 28,154
- L95
- 30
- %GC
- 40.08
- Ns
- 0
- gaps
- 0
- loci tagged
- 636
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 | 267 (38 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 24 (39 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 23 (39 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 267 (38 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 24 (39 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 23 (39 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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