Full information on isolate GDFK0402 (id:18603)
Provenance/primary metadata
- id
- 18603
- isolate
- GDFK0402
- sender
- xiaoyuan Jiang, CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- curator
- Auto Tagger
- update history
- 9 updates show details
- date entered
- 2021-12-12
- datestamp
- 2023-01-22
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2009
- city
- Beijing
- country
- China
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- NA
Sequence bin
- method
- Illumina
- contigs
- 184
- total length
- 5,444,513 bp
- max length
- 506,344 bp
- mean length
- 29,590 bp
- N50
- 272,231
- L50
- 8
- N90
- 48,618
- L90
- 28
- N95
- 31,135
- L95
- 35
- %GC
- 57.38
- Ns
- 1647
- gaps
- 17
- loci tagged
- 728
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
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 3
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 20-1LV
- Salmochelin
- iro 1
- SmST
- 14
- RmpADC
- rmp 1; KpVP-1
- RmST
- 26
- rmpA2
- rmpA2_2-54%
- wzi
- wzi72
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.40%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.98%
- Bla_chr
- SHV-1^
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 3*
- iroB
- 1
- iroC
- 1
- iroD
- 1
- iroN
- 3
- rmpA
- 2
- rmpD
- 2
- rmpC
- 2
Analysis performed: 2025-10-17; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_390_0_10_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL375
- Clonal group
- CG375
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_390_0_10_0 | 7 | 1 |
| 0_0_390_0_10_0_0 | 4 | 1 |
| 0_0_390_0_10_0_0_0 | 2 | 1 |
| 0_0_390_0_10_0_0_0_0 | 1 | 1 |
| 0_0_390_0_10_0_0_0_0_0 | 0 | 1 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_390 | 190 | 36 |
| 0_0_390_0 | 43 | 36 |
| 0_0_390_0_10 | 10 | 1 |
| 0_0_390_0_10_0 | 7 | 1 |
| 0_0_390_0_10_0_0 | 4 | 1 |
| 0_0_390_0_10_0_0_0 | 2 | 1 |
| 0_0_390_0_10_0_0_0_0 | 1 | 1 |
| 0_0_390_0_10_0_0_0_0_0 | 0 | 1 |
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_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) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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