Full information on isolate PLW-D33 (id:1542)
Provenance/primary metadata
- id
- 1542
- isolate
- PLW-D33
- biosample
- PRJDB16119
- accession number
- SAMD00626130
- clade
- P1
- species
- interrogans
- serogroup
- Icterohaemorrhagiae
- 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
- 5 updates show details
- date entered
- 2023-07-17
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 163
- total length
- 4,615,809 bp
- max length
- 350,268 bp
- mean length
- 28,318 bp
- N50
- 133,645
- L50
- 12
- N90
- 40,510
- L90
- 37
- N95
- 29,828
- L95
- 43
- %GC
- 35.02
- 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 | 545 | 100 | |
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 | 6 (146 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 6 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 58 (30 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 6 (36 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 6 (38 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 54 (36 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 6 (38 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 6 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 6 (34 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 6 (38 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 6 (146 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 6 (146 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 6 (146 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 6 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 58 (30 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 6 (36 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 6 (38 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 54 (36 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 6 (38 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 6 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 6 (34 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 6 (38 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 6 (146 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 6 (146 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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