Full information on isolate AMM-047 (id:1847)
Provenance/primary metadata
- id
- 1847
- isolate
- AMM-047
- biosample
- SAMD00754778
- clade
- P1
- species
- interrogans
- serogroup
- Hebdomadis
- serovar
- not examined
- isolation year
- 2020
- world region
- Eastern Asia
- country
- Japan
- host
- other
- sample type
- kidney
- source lab
- NIID
- sender
- Nobuo Koizumi, National institute of infectious diseases, Japan
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 6 updates show details
- date entered
- 2024-03-28
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 121
- total length
- 4,687,174 bp
- max length
- 586,642 bp
- mean length
- 38,737 bp
- N50
- 91,312
- L50
- 12
- N90
- 24,589
- L90
- 50
- N95
- 14,514
- L95
- 62
- %GC
- 35.04
- Ns
- 0
- gaps
- 0
- loci tagged
- 608
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 | 537 | 98 | |
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 | 472 (8 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 460 (8 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 485 (8 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 456 (8 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 443 (8 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 472 (8 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 460 (8 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 485 (8 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 456 (8 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 443 (8 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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