Full information on isolate leptoCuba22 (id:793)
Provenance/primary metadata
- id
- 793
- isolate
- leptoCuba22
- alias
- LI455
- clade
- P1
- species
- interrogans
- serogroup
- Icterohaemorrhagiae
- serovar
- Copenhageni
- isolation year
- 1991
- sequencing year
- 2019
- world region
- Caribbean
- country
- Cuba
- host
- rat
- sample type
- kidney
- source lab
- Finlay Institute of vaccine
- comments
- Pathogens
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 11 updates show details
- date entered
- 2019-11-13
- datestamp
- 2024-02-01
Sequence bin
- method
- Illumina
- contigs
- 155
- total length
- 4,566,756 bp
- max length
- 143,057 bp
- mean length
- 29,463 bp
- N50
- 53,253
- L50
- 29
- N90
- 18,144
- L90
- 80
- N95
- 11,731
- L95
- 95
- %GC
- 35.03
- 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 | 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
Export:
Analysis: