Full information on isolate cuba_10 (id:941)
Provenance/primary metadata
- id
- 941
- isolate
- cuba_10
- aliases
- 201900818; H-630.09
- clade
- P1
- species
- interrogans
- serogroup
- Canicola
- serovar
- Canicola
- isolation year
- 2009
- world region
- Caribbean
- country
- Cuba
- host
- human
- sample type
- Blood
- source lab
- IPK
- comments
- pathogen
- sender
- Jean-François Mariet, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 21 updates show details
- date entered
- 2019-04-08
- datestamp
- 2025-07-22
Sequence bin
- method
- Illumina
- contigs
- 256
- total length
- 4,643,306 bp
- max length
- 135,439 bp
- mean length
- 18,138 bp
- N50
- 41,464
- L50
- 34
- N90
- 10,791
- L90
- 114
- N95
- 7,276
- L95
- 140
- %GC
- 34.97
- Ns
- 0
- gaps
- 0
- loci tagged
- 609
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 | 28 (53 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 27 (14 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 32 (12 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 25 (14 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 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-75 | cgMLST | Single-linkage | 75 | experimental | 27 (14 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 32 (12 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 25 (14 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 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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