Full information on isolate 201800318 (id:681)
Provenance/primary metadata
- id
- 681
- isolate
- 201800318
- alias
- 17/OD2025
- clade
- P1
- species
- borgpetersenii
- serogroup
- Ballum
- serovar
- Unknown
- isolation year
- 2017
- sequencing year
- 2018
- world region
- Western Europe
- country
- Switzerland
- city
- Bern
- host
- other rodent
- sample type
- Kidney
- source lab
- Swiss National Reference Lab for a.
- comments
- Pathogen, MLST type ST149, mouse / Swiss National Reference Lab for animal leptospirosis
- sender
- Céline Lorioux, Institut Pasteur, Paris
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 23 updates show details
- date entered
- 2018-03-19
- datestamp
- 2024-04-17
Sequence bin
- contigs
- 136
- total length
- 3,821,069 bp
- max length
- 160,844 bp
- mean length
- 28,097 bp
- N50
- 64,565
- L50
- 19
- N90
- 19,408
- L90
- 64
- N95
- 13,686
- L95
- 75
- %GC
- 40.18
- Ns
- 0
- gaps
- 0
- loci tagged
- 610
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 | 540 | 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 | 15 (118 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (118 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 14 (80 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 13 (80 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 16 (80 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 13 (80 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (118 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (118 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (118 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 15 (118 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (118 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 14 (80 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 13 (80 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 16 (80 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 13 (80 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (118 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (118 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (118 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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