Full information on isolate E8 (id:1868)
Provenance/primary metadata
- id
- 1868
- isolate
- E8
- biosample
- SAMD00111974
- accession number
- ASM311267v1
- clade
- P2
- species
- johnsonii
- serogroup
- Unknown
- serovar
- unknown
- isolation year
- 2014
- sequencing year
- 2018
- world region
- Eastern Asia
- country
- Japan
- city
- Kamisu
- host
- environment
- sample type
- soil
- source lab
- Lab Parasitology Hokkaido Univ
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 4 updates show details
- date entered
- 2024-06-11
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 20
- total length
- 4,063,992 bp
- max length
- 1,754,512 bp
- mean length
- 203,200 bp
- N50
- 508,309
- L50
- 2
- N90
- 164,397
- L90
- 7
- N95
- 90,039
- L95
- 8
- %GC
- 41.26
- Ns
- 0
- gaps
- 0
- loci tagged
- 611
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 | 526 | 96 | |
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 | 221 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 216 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 203 (2 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 201 (2 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 239 (2 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 195 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 227 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 172 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 214 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 208 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 221 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 216 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 203 (2 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 201 (2 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 239 (2 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 195 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 227 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 172 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 214 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 208 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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