Full information on isolate PLW-D97 (id:1546)
Provenance/primary metadata
- id
- 1546
- isolate
- PLW-D97
- biosample
- PRJDB16119
- accession number
- SAMD00626134
- clade
- P1
- species
- interrogans
- serogroup
- Pyrogenes
- serovar
- not examined
- isolation year
- 2022
- 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
- 7 updates show details
- date entered
- 2023-07-17
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 203
- total length
- 4,985,727 bp
- max length
- 240,939 bp
- mean length
- 24,561 bp
- N50
- 63,664
- L50
- 22
- N90
- 16,574
- L90
- 73
- N95
- 5,753
- L95
- 95
- %GC
- 35.13
- 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 | 540 | 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 | 455 (13 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 445 (13 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 466 (13 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 293 (14 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 286 (14 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 455 (13 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 445 (13 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 466 (13 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 293 (14 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 286 (14 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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