Full information on isolate SB6662 (id:12324)
Projects
This isolate is a member of the following project:
- Delgado-Blas et al. 2025
- Collection of 336 isolates from different ecological sources (soil, WWTP, animals, clinical) recovered from July 2018 to July 2019. Preprint : Pangenome structure and ecological adaptation in the Klebsiella pneumoniae species complex: insights from a geographically and time limited multi-habitat study (doi: https://doi.org/10.64898/2025.12.11.693626)
Provenance/primary metadata
- id
- 12324
- isolate
- SB6662
- alias
- 12894
- sender
- Virginie Passet, Institut Pasteur, France
- curator
- Carla Rodrigues, Institut Pasteur, France (E-mail: carla.parada-rodrigues@pasteur.fr)
- update history
- 15 updates show details
- embargo history
- show details
- date entered
- 2020-03-19
- datestamp
- 2025-12-05
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Bourgogne-Franche-Comté region
- country
- France
- continent
- Europe
- source type
- Other
- host
- Environment
- source details
- fertilizer
- other source info
- Organic vegetable farm-Sample 11 - soil
- source lab
- INRAE Dijon
Sequence bin
- method
- Unknown
- contigs
- 53
- total length
- 5,257,224 bp
- max length
- 550,533 bp
- mean length
- 99,193 bp
- N50
- 293,981
- L50
- 7
- N90
- 61,556
- L90
- 21
- N95
- 43,102
- L95
- 26
- %GC
- 57.60
- Ns
- 0
- gaps
- 0
- loci tagged
- 706
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 | |||
| MLST | 7 | 7 | 100 | |
| Ribosomal MLST | 53 | 53 | 100 | |
| scgMLST629_S | 629 | 627 | 99 | |
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_46_5_2_0_0_0_1_0
- Phylogroup
- Kp1
- Sublineage
- SL76
- Clonal group
- CG10052
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 |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (68 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 348 (13 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (68 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 348 (13 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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