Full information on isolate 4-I (id:1224)
Provenance/primary metadata
- id
- 1224
- isolate
- 4-I
- alias
- 4-I
- biosample
- SAMN22220436
- accession number
- 13525301
- clade
- P1
- species
- borgpetersenii
- serogroup
- Unknown
- serovar
- Javanica
- isolation year
- 2012
- sequencing year
- 2021
- world region
- Central Asia
- country
- Russia
- city
- Irkutsk
- host
- Sorex tundrensis
- 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
- 6 updates show details
- date entered
- 2022-10-27
- datestamp
- 2024-04-25
Sequence bin
- contigs
- 2
- total length
- 3,939,236 bp
- max length
- 3,606,917 bp
- mean length
- 1,969,618 bp
- N50
- 3,606,917
- L50
- 1
- N90
- 3,606,917
- L90
- 1
- N95
- 332,319
- L95
- 2
- %GC
- 40.05
- 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 | 533 | 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 | 313 (5 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 305 (5 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 322 (5 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 302 (5 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 294 (19 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 313 (5 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 305 (5 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 322 (5 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 302 (5 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 294 (19 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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