Full information on isolate 445_IZSLER (id:1595)
Provenance/primary metadata
- id
- 1595
- isolate
- 445_IZSLER
- clade
- P1
- species
- interrogans
- serogroup
- Pomona
- serovar
- not examined
- isolation year
- 2017
- sequencing year
- 2023
- world region
- Western Europe
- country
- Italy
- host
- Unknown
- sample type
- urine
- source lab
- IZSLER
- sender
- Bertasio Cristina, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia (Italy)
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 5 updates show details
- date entered
- 2024-01-15
- datestamp
- 2024-04-17
Sequence bin
- method
- Illumina
- contigs
- 177
- total length
- 4,518,408 bp
- max length
- 239,230 bp
- mean length
- 25,528 bp
- N50
- 83,351
- L50
- 15
- N90
- 22,210
- L90
- 54
- N95
- 13,786
- L95
- 67
- %GC
- 34.92
- Ns
- 0
- gaps
- 0
- loci tagged
- 621
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 | 5 (74 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 5 (30 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 118 (23 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 5 (39 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 5 (39 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 5 (39 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 5 (41 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 5 (30 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 5 (74 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 5 (30 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 118 (23 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 5 (39 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 5 (39 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 5 (39 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 5 (41 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 5 (30 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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