Full information on isolate GCA_001720695.1 (id:47732)
Projects
This isolate is a member of the following project:
- Hennart_et_al_2022_full_collection
- Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230
Provenance/primary metadata
- id
- 47732
- isolate
- GCA_001720695.1
- alias
- CFSAN044574
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 5 updates show details
- date entered
- 2023-03-23
- datestamp
- 2024-05-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- The Netherlands
- continent
- Europe
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN05213504
Sequence bin
- contigs
- 45
- total length
- 5,322,619 bp
- max length
- 657,052 bp
- mean length
- 118,281 bp
- N50
- 356,097
- L50
- 6
- N90
- 94,365
- L90
- 16
- N95
- 74,732
- L95
- 19
- %GC
- 57.41
- Ns
- 0
- gaps
- 0
- loci tagged
- 705
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 | 624 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 2; ICEKp1
- YbST
- 321-1LV
- CbST
- 0
- AbST
- 0
- Salmochelin
- iro 3 (truncated)
- SmST
- 21
- RmpADC
- rmp 3; ICEKp1
- RmST
- 145
- wzi
- wzi2
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.72%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.81%
- Bla_chr
- SHV-1*
- spurious_resistance_hits
- fosA7*?-0%
- ybtS
- 8
- ybtX
- 55
- ybtQ
- 50
- ybtP
- 6
- ybtA
- 5
- irp2
- 117
- irp1
- 125
- ybtU
- 6
- ybtT
- 7
- ybtE
- 7
- fyuA
- 166
- iroB
- 6
- iroC
- 38-4%
- iroD
- 10
- iroN
- 5
- rmpA
- 20
- rmpD
- 1
- rmpC
- 1
Analysis performed: 2024-04-17; Kleborate v2.3.2
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 206 (6 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 303 (4 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 480 (4 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 206 (6 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 303 (4 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 480 (4 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 537 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 633 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 745 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 833 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 948 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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