Full information on isolate 202100567 (id:1149)
Provenance/primary metadata
- id
- 1149
- isolate
- 202100567
- alias
- Nenad Pomona2
- clade
- P1
- species
- kirschneri
- serogroup
- Pomona
- serovar
- Not examined
- isolation year
- 2001
- sequencing year
- 2021
- world region
- Eastern Europe
- country
- Croatia
- host
- Souris ?
- sample type
- Culture
- source lab
- CNR_leptospirose
- comments
- species obtained by cgMLST
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 14 updates show details
- date entered
- 2021-04-06
- datestamp
- 2024-04-17
Sequence bin
- method
- Illumina
- contigs
- 312
- total length
- 4,822,491 bp
- max length
- 190,266 bp
- mean length
- 15,457 bp
- N50
- 32,538
- L50
- 43
- N90
- 9,046
- L90
- 149
- N95
- 5,628
- L95
- 181
- %GC
- 35.86
- Ns
- 22
- gaps
- 19
- loci tagged
- 599
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 | 537 | 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 | 73 (22 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 70 (22 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 75 (22 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 70 (22 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 66 (22 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 73 (22 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 70 (22 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 75 (22 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 70 (22 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 66 (22 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: