Full information on isolate PLW-D34 (id:1543)
Provenance/primary metadata
- id
- 1543
- isolate
- PLW-D34
- biosample
- PRJDB16119
- accession number
- SAMD00626131
- clade
- P1
- species
- interrogans
- serogroup
- not examined
- serovar
- not examined
- isolation year
- 2021
- sequencing year
- 2023
- passage
- ?
- world region
- Micronesia
- country
- Palau
- host
- dog
- sample type
- Blood
- 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
- 8 updates show details
- date entered
- 2023-07-17
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 283
- total length
- 4,816,219 bp
- max length
- 333,616 bp
- mean length
- 17,019 bp
- N50
- 75,814
- L50
- 18
- N90
- 18,688
- L90
- 65
- N95
- 9,617
- L95
- 84
- %GC
- 35.10
- Ns
- 0
- gaps
- 0
- loci tagged
- 547
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 | 538 | 98 | |
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 |
|---|---|---|---|---|---|
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 428 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 454 (1 isolate) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 444 (1 isolate) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 465 (1 isolate) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 441 (1 isolate) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 428 (2 isolates) |
Schemes and loci
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