Full information on isolate D64 (id:1277)
Provenance/primary metadata
- id
- 1277
- isolate
- D64
- biosample
- SAMN13679794
- clade
- P1
- species
- interrogans
- serogroup
- Unknown
- serovar
- Bataviae
- isolation year
- 2017
- sequencing year
- 2022
- world region
- South-eastern Asia
- country
- Thailand
- city
- Bangkok
- host
- dog
- sample type
- Urine
- source lab
- GenBank
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 11 updates show details
- date entered
- 2022-09-12
- datestamp
- 2024-04-17
Sequence bin
- method
- Illumina + ONT hybrid (3 contigs)
other (1 contig) - contigs
- 4
- total length
- 4,846,851 bp
- max length
- 4,355,742 bp
- mean length
- 1,211,713 bp
- N50
- 4,355,742
- L50
- 1
- N90
- 359,451
- L90
- 2
- N95
- 359,451
- L95
- 2
- %GC
- 35.16
- Ns
- 0
- gaps
- 0
- loci tagged
- 622
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 | 544 | 99 | |
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
Tools
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