Full information on isolate SB6469 (id:9524)
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
- 9524
- isolate
- SB6469
- alias
- MVK-03E148
- sender
- Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
- curator
- Carla Rodrigues, Institut Pasteur, France (E-mail: carla.parada-rodrigues@pasteur.fr)
- update history
- 18 updates show details
- embargo history
- show details
- date entered
- 2019-08-08
- 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
- Environment
- host
- Environment
- source details
- roots
- other source info
- Organic vegetable farm-Sample 19 - parsley roots
- source lab
- INRAE Dijon
Sequence bin
- method
- Illumina
- contigs
- 67
- total length
- 5,240,566 bp
- max length
- 450,967 bp
- mean length
- 78,218 bp
- N50
- 179,432
- L50
- 10
- N90
- 48,421
- L90
- 33
- N95
- 27,864
- L95
- 40
- %GC
- 57.72
- Ns
- 0
- gaps
- 0
- loci tagged
- 713
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 | 629 | 100 | |
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_927_0_0_0_0_2_0_1
- Phylogroup
- Kp1
- Sublineage
- SL10860
- Clonal group
- CG11546
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_927_0_0_0 | 7 | 12 |
| 0_0_927_0_0_0_0 | 4 | 12 |
| 0_0_927_0_0_0_0_2 | 2 | 10 |
| 0_0_927_0_0_0_0_2_0 | 1 | 10 |
| 0_0_927_0_0_0_0_2_0_1 | 0 | 8 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_927 | 190 | 16 |
| 0_0_927_0 | 43 | 16 |
| 0_0_927_0_0 | 10 | 16 |
| 0_0_927_0_0_0 | 7 | 12 |
| 0_0_927_0_0_0_0 | 4 | 12 |
| 0_0_927_0_0_0_0_2 | 2 | 10 |
| 0_0_927_0_0_0_0_2_0 | 1 | 10 |
| 0_0_927_0_0_0_0_2_0_1 | 0 | 8 |
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 | 1558 (11 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2621 (11 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 | 1558 (11 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2621 (11 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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