Full information on isolate GCA_003860845.1 (id:53832)
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
- 53832
- isolate
- GCA_003860845.1
- alias
- KLPN_M84
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 4 updates show details
- date entered
- 2023-04-03
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- USA
- continent
- North America
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN10241293
Sequence bin
- contigs
- 4
- total length
- 5,728,832 bp
- max length
- 5,387,449 bp
- mean length
- 1,432,208 bp
- N50
- 5,387,449
- L50
- 1
- N90
- 5,387,449
- L90
- 1
- N95
- 147,373
- L95
- 2
- %GC
- 57.09
- Ns
- 0
- gaps
- 0
- loci tagged
- 710
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 | 621 | 98 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 2
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 6; ICEKp5
- YbST
- 62-6LV
- Colibactin
- clb 3
- CbST
- 13
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.54%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.61%
- Bla_chr
- SHV-1
- ybtS
- 22
- ybtX
- 22
- ybtQ
- 6
- ybtP
- 24
- ybtA
- 16
- irp2
- 366
- irp1
- 455
- ybtU
- 113
- ybtT
- 11
- ybtE
- 4
- fyuA
- 2
- clbA
- 2
- clbB
- 10
- clbC
- 2
- clbD
- 2
- clbE
- 2
- clbF
- 2
- clbG
- 2
- clbH
- 3
- clbI
- 2
- clbL
- 2
- clbM
- 2
- clbN
- 2
- clbO
- 2
- clbP
- 2
- clbQ
- 2
Analysis performed: 2024-04-26; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_5_1_0_0_0_0_0
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 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 95 (43 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 115 (5 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 95 (43 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 115 (5 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1277 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 1438 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 1757 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2171 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 2529 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 3075 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: