Full information on isolate Ag03_2020 (id:1035)
Provenance/primary metadata
- id
- 1035
- isolate
- Ag03_2020
- aliases
- Ag3_Bataviae; Van Tienen
- biosample
- P1
- clade
- P1
- species
- interrogans
- serogroup
- Bataviae
- serovar
- Bataviae
- sequencing year
- 2020
- world region
- Western Europe
- country
- France
- host
- unknown
- sample type
- Culture
- source lab
- CNR_leptospirose
- comments
- 2020 contrôle annuel Ag diag
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 20 updates show details
- date entered
- 2020-03-26
- datestamp
- 2025-05-12
Sequence bin
- method
- Illumina
- contigs
- 359
- total length
- 3,937,628 bp
- max length
- 70,012 bp
- mean length
- 10,969 bp
- N50
- 19,676
- L50
- 67
- N90
- 6,054
- L90
- 204
- N95
- 3,968
- L95
- 243
- %GC
- 35.59
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,086
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | N50 too low (warn threshold: 20,000) | |
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 508 | 93 | |
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 | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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