Full information on isolate 56601 (id:27)
Provenance/primary metadata
- id
- 27
- isolate
- 56601
- biosample
- SAMN02603127
- accession number
- ASM9256v1
- clade
- P1
- species
- interrogans
- serogroup
- Icterohaemorrhagiae
- serovar
- Lai
- sequencing year
- 2003
- world region
- Eastern Asia
- country
- China
- host
- human
- sample type
- Unknown
- 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
- 1869 updates show details
- date entered
- 2016-12-01
- datestamp
- 2024-04-17
Publications (3)
- 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
- Ren SX, Fu G, Jiang XG, Zeng R, Miao YG, Xu H, Zhang YX, Xiong H, Lu G, Lu LF, Jiang HQ, Jia J, Tu YF, Jiang JX, Gu WY, Zhang YQ, Cai Z, Sheng HH, Yin HF, Zhang Y, Zhu GF, Wan M, Huang HL, Qian Z, Wang SY, Ma W, Yao ZJ, Shen Y, Qiang BQ, Xia QC, Guo XK, Danchin A, Saint Girons I, Somerville RL, Wen YM, Shi MH, Chen Z, Xu JG, Zhao GP (2003). Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature 422:888-93
Sequence bin
- contigs
- 2
- total length
- 4,698,134 bp
- max length
- 4,338,762 bp
- mean length
- 2,349,067 bp
- N50
- 4,338,762
- L50
- 1
- N90
- 4,338,762
- L90
- 1
- N95
- 359,372
- L95
- 2
- %GC
- 35.02
- Ns
- 0
- gaps
- 0
- loci tagged
- 613
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 | 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 | 16 (3 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 16 (3 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 16 (3 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 16 (3 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 15 (3 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 16 (3 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 16 (3 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 16 (3 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 16 (3 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 15 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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