Full information on isolate FH4-C-A2 (id:1866)
Provenance/primary metadata
- id
- 1866
- isolate
- FH4-C-A2
- biosample
- SAMN07411425
- accession number
- ASM281176v1
- clade
- P2
- species
- saintgironsiae
- serogroup
- Unknown
- serovar
- unknown
- isolation year
- 2016
- world region
- Melanesia
- country
- New Caledonia
- host
- soil
- sample type
- Culture
- source lab
- Institut Pasteur Montevideo
- 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
Publication (1)
- Thibeaux R, Iraola G, Ferrés I, Bierque E, Girault D, Soupé-Gilbert ME, Picardeau M, Goarant C (2018). Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence. Microb Genom 4:
Sequence bin
- contigs
- 42
- total length
- 4,083,319 bp
- max length
- 1,069,366 bp
- mean length
- 97,222 bp
- N50
- 551,160
- L50
- 3
- N90
- 96,033
- L90
- 10
- N95
- 45,315
- L95
- 13
- %GC
- 39.11
- Ns
- 0
- gaps
- 0
- loci tagged
- 596
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 | 522 | 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 | 341 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 333 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 352 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 330 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 322 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 341 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 333 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 352 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 330 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 322 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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