Full information on isolate MAVJ401 (id:1310)
Provenance/primary metadata
- id
- 1310
- isolate
- MAVJ401
- alias
- MAVJ 401
- biosample
- SAMN02436499
- accession number
- GCA_000243835.3
- clade
- P1
- species
- santarosai
- serogroup
- Javanica
- serovar
- Arenal
- isolation year
- 2013
- sequencing year
- 2013
- world region
- Central America
- country
- Costa Rica
- city
- Alajuela province
- host
- human
- sample type
- Unknown
- source lab
- GenBank
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 10 updates show details
- date entered
- 2022-10-12
- datestamp
- 2024-04-25
Sequence bin
- contigs
- 87
- total length
- 4,245,663 bp
- max length
- 373,662 bp
- mean length
- 48,801 bp
- N50
- 134,699
- L50
- 9
- N90
- 31,063
- L90
- 34
- N95
- 16,615
- L95
- 44
- %GC
- 41.56
- Ns
- 0
- gaps
- 0
- loci tagged
- 600
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 | 531 | 97 | |
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 | 54 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 53 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 56 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 53 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 51 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 54 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 53 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 56 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 53 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 51 (2 isolates) |
Schemes and loci
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