Full information on isolate leptoCuba23 (id:794)
Provenance/primary metadata
- id
- 794
- isolate
- leptoCuba23
- alias
- LCF2004
- clade
- P1
- species
- interrogans
- serogroup
- Canicola
- serovar
- Canicola
- isolation year
- 1988
- sequencing year
- 2019
- world region
- Caribbean
- country
- Cuba
- host
- bovine
- sample type
- urine
- source lab
- Finlay Institute of vaccine
- comments
- Pathogens
- sender
- Jean-François Mariet, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 13 updates show details
- date entered
- 2019-11-13
- datestamp
- 2025-07-22
Sequence bin
- method
- Illumina
- contigs
- 301
- total length
- 4,525,201 bp
- max length
- 119,945 bp
- mean length
- 15,034 bp
- N50
- 31,413
- L50
- 48
- N90
- 8,407
- L90
- 152
- N95
- 5,063
- L95
- 185
- %GC
- 35.10
- Ns
- 0
- gaps
- 0
- loci tagged
- 601
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 | 543 | 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 | 28 (53 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 28 (53 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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