Full information on isolate GCA_004005105.1 (id:46783)
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
- 46783
- isolate
- GCA_004005105.1
- alias
- 064C6
- 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
- France
- continent
- Europe
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN10644715
Sequence bin
- contigs
- 166
- total length
- 5,586,881 bp
- max length
- 376,325 bp
- mean length
- 33,656 bp
- N50
- 152,313
- L50
- 13
- N90
- 26,100
- L90
- 43
- N95
- 13,409
- L95
- 57
- %GC
- 57.22
- Ns
- 4889
- gaps
- 45
- loci tagged
- 701
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 | 627 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 2
- num_resistance_classes
- 1
- num_resistance_genes
- 1
- Yersiniabactin
- ybt 4; plasmid
- YbST
- 31-1LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi23
- K_locus
- unknown (KL35)
- K_type
- unknown (K35)
- K_locus_problems
- ?-+
- K_locus_confidence
- None
- K_locus_identity
- 99.15%
- K_locus_missing_genes
- KL35_06_wzc,KL35_07_wzy,KL35_08_wcuC,KL35_09_wckM,KL35_10_wckL,KL35_11_wcuQ,KL35_12_wzx,KL35_14_wbaZ,KL35_15_wcaJ,KL35_16_wclK,KL35_19_manB
- O_locus
- O5
- O_type
- O5
- O_locus_problems
- ?-*
- O_locus_confidence
- Good
- O_locus_identity
- 94.22%
- O_locus_missing_genes
- O5_02_manB
- Bla_Carb_acquired
- OXA-48
- Bla_chr
- SHV-1^
- ybtS
- 18
- ybtX
- 20
- ybtQ
- 27
- ybtP
- 18
- ybtA
- 13
- irp2
- 81
- irp1
- 38
- ybtU
- 9
- ybtT
- 8
- ybtE
- 78
- fyuA
- 35
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 | 52 (57 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 54 (13 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 | 52 (57 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 54 (13 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 55 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 57 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 59 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 60 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 61 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 61 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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