Full information on isolate GCA_000529775.1 (id:52000)
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
- 52000
- isolate
- GCA_000529775.1
- alias
- T69
- sender
- Mélanie Hennart, Institut Pasteur, France
- 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
- Unknown
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMEA3138865
Sequence bin
- method
- Unknown
- contigs
- 1
- length
- 5,486,528 bp
- %GC
- 57.26
- Ns
- 23300
- gaps
- 233
- loci tagged
- 685
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 | 625 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 4
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 5; ICEKp6? (truncated)
- YbST
- 12
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 20
- Salmochelin
- iro 1
- SmST
- 14
- RmpADC
- rmp 1; KpVP-1 (truncated)
- RmST
- 27
- rmpA2
- rmpA2_5-54%
- wzi
- wzi72
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.39%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.96%
- Bla_chr
- SHV-1^
- ybtS
- 10
- ybtX
- 8
- ybtQ
- 10
- ybtP
- 7
- ybtA
- 6
- irp2
- 4
- irp1
- 4-87%
- ybtU
- 7
- ybtT
- 8
- ybtE
- 5
- fyuA
- 7
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 3
- iroB
- 1
- iroC
- 1
- iroD
- 1
- iroN
- 3
- rmpA
- 4-47%
- rmpD
- 2
- rmpC
- 2
Analysis performed: 2024-04-26; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_390_0_6_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL375
- Clonal group
- CG375
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 | 41 (25 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 41 (25 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1611 (2 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 1828 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2244 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2803 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3288 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4085 (2 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 | 41 (25 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 41 (25 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1611 (2 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 1828 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2244 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2803 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3288 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4085 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: