Full information on isolate 201000851 (id:163)
Provenance/primary metadata
- id
- 163
- isolate
- 201000851
- biosample
- SAMN02436414
- accession number
- 1049776
- clade
- P1
- species
- borgpetersenii
- serogroup
- Mini
- serovar
- Mini
- sequencing year
- 2012
- world region
- Eastern Africa
- country
- Mayotte
- host
- human
- sample type
- Blood
- source lab
- Craig Venter Institute
- sender
- Julien Guglielmini, Institut Pasteur
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 981 updates show details
- date entered
- 2016-12-01
- datestamp
- 2024-04-17
Sequence bin
- contigs
- 72
- total length
- 4,000,282 bp
- max length
- 318,939 bp
- mean length
- 55,560 bp
- N50
- 103,763
- L50
- 13
- N90
- 33,395
- L90
- 39
- N95
- 18,807
- L95
- 47
- %GC
- 40.23
- Ns
- 1
- gaps
- 1
- loci tagged
- 1,100
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 | 486 | 89 | |
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 | 78 (50 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 70 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 74 (50 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 95 (33 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 68 (49 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 67 (49 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 88 (48 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 64 (49 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 63 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 8 (37 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 84 (50 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 74 (50 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 69 (50 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 78 (50 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 70 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 74 (50 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 95 (33 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 68 (49 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 67 (49 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 88 (48 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 64 (49 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 63 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 8 (37 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 84 (50 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 74 (50 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 69 (50 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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