Full information on isolate GCA_900451725.1 (id:51106)
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
- 51106
- isolate
- GCA_900451725.1
- alias
- NCTC1936
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 4 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-04-14
- 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
- SAMEA3400773
Sequence bin
- contigs
- 2
- total length
- 5,505,946 bp
- max length
- 5,401,175 bp
- mean length
- 2,752,973 bp
- N50
- 5,401,175
- L50
- 1
- N90
- 5,401,175
- L90
- 1
- N95
- 5,401,175
- L95
- 1
- %GC
- 57.09
- Ns
- 0
- gaps
- 0
- loci tagged
- 660
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 | 600 | 95 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 4
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 11; ICE_rhino (truncated)
- YbST
- 310-1LV
- CbST
- 0
- Aerobactin
- iuc 4
- AbST
- 52
- SmST
- 0
- RmpADC
- rmp 4; chromosomal
- RmST
- 62
- wzi
- wzi135
- K_locus
- KL3
- K_type
- K3
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.49%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.52%
- O_locus_missing_genes
- O1/O2v2_08_gmlC,O1/O2v2_09_gmlB
- Bla_chr
- SHV-206
- ybtS
- 6
- ybtX
- 6
- ybtQ
- 7
- ybtP
- 86
- ybtA
- 1
- irp2
- 10-11%
- irp1
- 219
- ybtU
- 5
- ybtT
- 6
- ybtE
- 6
- fyuA
- 107*-25%
- iucA
- 26
- iucB
- 5
- iucC
- 4
- iucD
- 24
- iutA
- 5
- iroC
- 7-4%
- rmpA
- 8
- rmpD
- 39
- rmpC
- 15
- spurious_virulence_hits
- iroD_9*-56%
Analysis performed: 2024-04-25; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_443_0_0_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 | 730 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1200 (2 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 | 730 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1200 (2 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2166 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2429 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2893 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3502 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4018 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4936 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
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Analysis: