Full information on isolate PLW-D49 (id:1544)
Provenance/primary metadata
- id
- 1544
- isolate
- PLW-D49
- biosample
- PRJDB16119
- accession number
- SAMD00626132
- 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
- 175
- total length
- 4,618,715 bp
- max length
- 350,308 bp
- mean length
- 26,393 bp
- N50
- 133,670
- L50
- 11
- N90
- 39,271
- L90
- 38
- N95
- 21,164
- L95
- 46
- %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 | 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 | 6 (146 isolates) |
Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 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-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 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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