Full information on isolate GCA_003687895.1 (id:46786)
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
- 46786
- isolate
- GCA_003687895.1
- alias
- 1002865
- 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
- Mexico
- continent
- North America
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN10252232
Sequence bin
- contigs
- 600
- total length
- 5,685,587 bp
- max length
- 74,582 bp
- mean length
- 9,476 bp
- N50
- 20,284
- L50
- 84
- N90
- 5,176
- L90
- 291
- N95
- 3,294
- L95
- 358
- %GC
- 56.92
- Ns
- 0
- gaps
- 0
- loci tagged
- 682
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| 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 | 616 | 97 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 9
- num_resistance_genes
- 12
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi187
- K_locus
- unknown (KL27)
- K_type
- unknown (K27)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.16%
- K_locus_missing_genes
- KL27_07_wcaJ,KL27_08_wckI,KL27_09_wckS,KL27_10_wckR,KL27_11_wzy,KL27_12_wzx,KL27_13_wckQ,KL27_14_wcuJ,KL27_15_wctE,KL27_16_wctF
- O_locus
- unknown (O4)
- O_type
- unknown (O4)
- O_locus_problems
- ?-
- O_locus_confidence
- Low
- O_locus_identity
- 99.74%
- O_locus_missing_genes
- O4_03_hypothetical,O4_05_wzm,O4_06_glycosyltransferase
- AGly_acquired
- aac(6')-Ib-cr.v2;strA.v1^;strB.v1
- Flq_acquired
- qnrB1.v2^
- Phe_acquired
- CatB4.v1?
- Sul_acquired
- sul2
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- NDM-1
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- Flq_mutations
- GyrA-83I;ParC-80I
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 | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (733 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 58 (56 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 155 (56 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 62 (40 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 63 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 64 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 64 (2 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 | 51 (733 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 58 (56 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 155 (56 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 62 (40 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 63 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 64 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 64 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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