Full information on isolate 4E (id:1877)
Provenance/primary metadata
- id
- 1877
- isolate
- 4E
- biosample
- SAMN04868324
- accession number
- ASM165252v2
- clade
- P1
- species
- borgpetersenii
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 2011
- sequencing year
- 2017
- world region
- South America
- country
- Brazil
- host
- Mouse
- sample type
- Unknown
- source lab
- CDTec
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 19 updates show details
- date entered
- 2024-10-03
- datestamp
- 2025-04-17
Sequence bin
- method
- Unknown
- contigs
- 2
- total length
- 3,912,599 bp
- max length
- 3,550,837 bp
- mean length
- 1,956,300 bp
- N50
- 3,550,837
- L50
- 1
- N90
- 3,550,837
- L90
- 1
- N95
- 361,762
- L95
- 2
- %GC
- 40.19
- Ns
- 603
- gaps
- 259
- loci tagged
- 598
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 | 523 | 95 | |
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 | 15 (116 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (116 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (116 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (116 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (116 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 15 (116 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (116 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (116 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (116 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (116 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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