Full information on isolate GCA_003427195.1 (id:51138)
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
- 51138
- isolate
- GCA_003427195.1
- alias
- ntmc-NN
- 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
- Unknown
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMD00131360
Sequence bin
- contigs
- 344
- total length
- 5,846,415 bp
- max length
- 129,425 bp
- mean length
- 16,996 bp
- N50
- 30,402
- L50
- 54
- N90
- 8,092
- L90
- 189
- N95
- 5,190
- L95
- 234
- %GC
- 56.54
- Ns
- 0
- gaps
- 0
- loci tagged
- 680
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 | 620 | 98 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 5
- num_resistance_genes
- 6
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi81
- K_locus
- unknown (KL81)
- K_type
- unknown (K81)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.98%
- K_locus_missing_genes
- KL81_06_wzc,KL81_10_wclJ,KL81_12_wcqM,KL81_14_wzx
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.45%
- O_locus_missing_genes
- O1/O2v2_10_gmlA
- AGly_acquired
- aac(6')-IIc
- Flq_acquired
- qnrB6^
- Sul_acquired
- sul1
- Tet_acquired
- tet(B).v2*;tetR
- Bla_Carb_acquired
- IMP-1
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK36-71%
- spurious_resistance_hits
- fosA7*?-0%
Analysis performed: 2024-04-25; 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 (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 | 43 (28 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 227 (8 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 | 43 (28 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 227 (8 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1424 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 1606 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 1967 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2450 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 2863 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 3516 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: