Full information on isolate 201800031 (id:620)
Provenance/primary metadata
- id
- 620
- isolate
- 201800031
- alias
- Abduloev
- clade
- P1
- species
- interrogans
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 2008
- passage
- 36
- world region
- Central Asia
- country
- Russia
- city
- St Petersburg
- host
- human
- sample type
- Blood
- source lab
- IP Saint Petersburg
- comments
- Abduloev (346) Pathogen
- sender
- Olivier Schiettekatte, Institut Pasteur
- curator
- Auto Tagger
- update history
- 25 updates show details
- date entered
- 2018-02-02
- datestamp
- 2025-07-22
Sequence bin
- method
- Illumina
- contigs
- 463
- total length
- 4,157,912 bp
- max length
- 57,307 bp
- mean length
- 8,981 bp
- N50
- 16,115
- L50
- 80
- N90
- 4,499
- L90
- 262
- N95
- 3,042
- L95
- 317
- %GC
- 35.56
- Ns
- 19
- gaps
- 2
- loci tagged
- 617
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | N50 too low (warn threshold: 20,000) | |
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 536 | 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 | 28 (53 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 28 (53 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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