Full information on isolate GCA_004004775.1 (id:46782)
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
- 46782
- isolate
- GCA_004004775.1
- alias
- 064B6
- 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
- SAMN10644705
Sequence bin
- contigs
- 318
- total length
- 5,938,709 bp
- max length
- 263,070 bp
- mean length
- 18,676 bp
- N50
- 105,875
- L50
- 18
- N90
- 13,544
- L90
- 73
- N95
- 5,102
- L95
- 108
- %GC
- 56.85
- Ns
- 7205
- gaps
- 71
- loci tagged
- 688
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 | 624 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 2
- num_resistance_genes
- 1
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi64
- K_locus
- unknown (KL64)
- K_type
- unknown (K64)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.97%
- K_locus_missing_genes
- KL64_06_wzc,KL64_07_wzx,KL64_08_wcoV,KL64_09,KL64_10_wzy,KL64_11_wcoU,KL64_12_wcoT,KL64_13_wcsF,KL64_14_wcuK,KL64_15_wbaZ,KL64_16_wcaJ
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.64%
- O_locus_missing_genes
- O1/O2v1_06_wbbO
- Bla_Carb_acquired
- OXA-48
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- CTX-M-162?-0%
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 | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 53 (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 | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 53 (3 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 54 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 56 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 58 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 59 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 60 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 60 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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