Full information on isolate 2002009669 (id:208)
Provenance/primary metadata
- id
- 208
- isolate
- 2002009669
- biosample
- SAMN01920624
- accession number
- 1291318
- clade
- P1
- species
- interrogans
- serogroup
- Icterohaemorrhagiae
- serovar
- Copenhageni
- sequencing year
- 2013
- world region
- Northern America
- country
- USA
- host
- human
- sample type
- Unknown
- source lab
- Craig Venter Institute
- sender
- Julien Guglielmini, Institut Pasteur
- curator
- Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
- update history
- 1059 updates show details
- date entered
- 2016-12-01
- datestamp
- 2023-02-02
Publications (2)
- Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M (2019). Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 13:e0007374
- Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M (2020). Correction: Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 14:e0008673
Sequence bin
- method
- Unknown
- contigs
- 155
- total length
- 4,572,939 bp
- max length
- 215,690 bp
- mean length
- 29,503 bp
- N50
- 49,767
- L50
- 25
- N90
- 13,709
- L90
- 91
- N95
- 9,880
- L95
- 111
- %GC
- 35.01
- Ns
- 0
- gaps
- 0
- loci tagged
- 620
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 | 543 | 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 | 6 (146 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 6 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 58 (30 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 6 (36 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 6 (38 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 54 (36 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 6 (38 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 6 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 6 (34 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 6 (38 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 6 (146 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 6 (146 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 6 (146 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 6 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 58 (30 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 6 (36 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 6 (38 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 54 (36 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 6 (38 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 6 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 6 (34 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 6 (38 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 6 (146 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 6 (146 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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