Full information on isolate E30 (id:1871)
Provenance/primary metadata
- id
- 1871
- isolate
- E30
- biosample
- SAMD00111976
- accession number
- ASM311483v3
- clade
- S2
- species
- kobayashii
- serogroup
- Unknown
- serovar
- unknown
- isolation year
- 2014
- sequencing year
- 2021
- world region
- Eastern Asia
- country
- Japan
- city
- gifu
- host
- environment
- sample type
- soil
- source lab
- Lab Parasitology Hokkaido Univ
- comments
- 201905847
- 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
- 2024-06-27
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 3
- total length
- 4,304,943 bp
- max length
- 3,985,339 bp
- mean length
- 1,434,981 bp
- N50
- 3,985,339
- L50
- 1
- N90
- 3,985,339
- L90
- 1
- N95
- 274,191
- L95
- 2
- %GC
- 40.69
- Ns
- 0
- gaps
- 0
- loci tagged
- 589
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 | 525 | 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 | 223 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 218 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 205 (2 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 203 (2 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 241 (2 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 197 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 229 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 174 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 216 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 210 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 223 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 218 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 205 (2 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 203 (2 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 241 (2 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 197 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 229 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 174 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 216 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 210 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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