Full information on isolate 202202042 (id:1285)
Provenance/primary metadata
- id
- 1285
- isolate
- 202202042
- alias
- 2013-VF52
- biosample
- SAMN34670627
- clade
- P1
- species
- santarosai
- serogroup
- Sejroe
- serovar
- Sejroe
- isolation year
- 2013
- sequencing year
- 2022
- world region
- South America
- country
- Brazil
- host
- bovine
- sample type
- Culture
- source lab
- Universidade Federal Fluminense
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 12 updates show details
- date entered
- 2022-10-07
- datestamp
- 2024-04-30
Sequence bin
- contigs
- 115
- total length
- 3,980,734 bp
- max length
- 274,417 bp
- mean length
- 34,616 bp
- N50
- 100,276
- L50
- 14
- N90
- 21,571
- L90
- 41
- N95
- 13,044
- L95
- 53
- %GC
- 41.84
- Ns
- 0
- gaps
- 0
- loci tagged
- 584
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 | 338 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 330 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 349 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 327 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 319 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 338 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 330 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 349 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 327 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 319 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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