Full information on isolate 2ACAP (id:1329)
Provenance/primary metadata
- id
- 1329
- isolate
- 2ACAP
- alias
- 2ACAP
- biosample
- SAMN06212382
- accession number
- GCF_001981425.1
- clade
- P1
- species
- santarosai
- serogroup
- Grippotyphosa
- serovar
- Bananal
- isolation year
- 2001
- sequencing year
- 2017
- world region
- South America
- country
- Brazil
- city
- Sao Paulo state
- host
- capybara
- sample type
- kidney
- 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
- 11 updates show details
- date entered
- 2022-10-12
- datestamp
- 2024-04-25
Sequence bin
- method
- other
- contigs
- 44
- total length
- 4,088,850 bp
- max length
- 421,432 bp
- mean length
- 92,929 bp
- N50
- 203,677
- L50
- 8
- N90
- 52,977
- L90
- 24
- N95
- 38,462
- L95
- 28
- %GC
- 41.73
- Ns
- 9
- gaps
- 9
- 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 | 525 | 96 | |
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 | 415 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 405 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 426 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 402 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 391 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 415 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 405 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 426 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 402 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 391 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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