Full information on isolate R123 (id:110)
Provenance/primary metadata
- id
- 110
- isolate
- R123
- alias
- R123
- biosample
- SAMN05467253
- accession number
- 13525201
- clade
- P1
- species
- interrogans
- serogroup
- Unknown
- serovar
- Bataviae
- isolation year
- 2011
- sequencing year
- 2016
- world region
- South-eastern Asia
- country
- Malaysia
- host
- rat
- sample type
- Kidney
- source lab
- Genbank
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Auto Tagger
- update history
- 10 updates show details
- date entered
- 2022-10-27
- datestamp
- 2025-04-10
Sequence bin
- method
- other
- contigs
- 353
- total length
- 4,804,613 bp
- max length
- 77,157 bp
- mean length
- 13,611 bp
- N50
- 26,989
- L50
- 59
- N90
- 6,991
- L90
- 187
- N95
- 4,019
- L95
- 230
- %GC
- 35.15
- Ns
- 38
- gaps
- 38
- loci tagged
- 595
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 | 538 | 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 | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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