Full information on isolate GCA_900635995.1 (id:46769)
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
- 46769
- isolate
- GCA_900635995.1
- alias
- NCTC418
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 3 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-03-24
- 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
- SAMEA3368254
Sequence bin
- contigs
- 4
- total length
- 5,560,297 bp
- max length
- 5,306,679 bp
- mean length
- 1,390,075 bp
- N50
- 5,306,679
- L50
- 1
- N90
- 5,306,679
- L90
- 1
- N95
- 5,306,679
- L95
- 1
- %GC
- 57.18
- Ns
- 0
- gaps
- 0
- loci tagged
- 687
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 | 52 | 98 | |
| scgMLST629_S | 629 | 615 | 97 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 3
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 20
- Salmochelin
- iro 1
- SmST
- 14
- RmpADC
- rmp 1; KpVP-1 (truncated)
- RmST
- 26-1LV
- rmpA2
- rmpA2_5-54%
- wzi
- wzi72
- K_locus
- KL2
- K_type
- K2
- K_locus_confidence
- High
- K_locus_identity
- 98.39%
- K_locus_missing_genes
- KL2_11_wzx
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_confidence
- High
- O_locus_identity
- 98.97%
- O_locus_missing_genes
- O1/O2v2_05_wbbN
- Bla_chr
- SHV-1^
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 3
- iroB
- 1
- iroC
- 1
- iroD
- 1
- iroN
- 3
- rmpA
- 2
- rmpD
- 2
- rmpC
- 2*-21%
Analysis performed: 2024-04-17; Kleborate v2.3.2
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 (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 | 41 (24 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 41 (24 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 41 (8 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 43 (5 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 44 (5 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 45 (4 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 46 (4 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 46 (3 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 | 41 (24 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 41 (24 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 41 (8 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 43 (5 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 44 (5 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 45 (4 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 46 (4 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 46 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: