Full information on isolate QMP_M1-200 (id:3069)
Projects
Provenance/primary metadata
- id
- 3069
- isolate
- QMP_M1-200
- sender
- Kat Holt, Melbourne U
- curator
- Auto Tagger
- update history
- 25 updates show details
- date entered
- 2015-06-01
- datestamp
- 2023-01-20
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2005
- country
- USA
- continent
- North America
- source type
- Food
- host
- Bovine
- source details
- Milk
- infection
- Bovine_infection
- other source info
- sterile
- source lab
- Ruth Zadoks
- accession number
- ERS011950
Publication (1)
- Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR (2015). Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 112:E3574-81
Sequence bin
- contigs
- 155
- total length
- 5,490,842 bp
- max length
- 431,905 bp
- mean length
- 35,425 bp
- N50
- 150,735
- L50
- 13
- N90
- 31,033
- L90
- 41
- N95
- 17,934
- L95
- 53
- %GC
- 57.30
- Ns
- 4267
- gaps
- 72
- loci tagged
- 3,926
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 | 626 | 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
- 0
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi11
- K_locus
- KL11
- K_type
- K11
- K_locus_problems
- *
- K_locus_confidence
- High
- K_locus_identity
- 92.41%
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- *
- O_locus_confidence
- Very high
- O_locus_identity
- 95.53%
- Bla_chr
- SHV-1^
Analysis performed: 2024-02-20; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_398_0_4_0_0_0_0_0
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 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 40 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 40 (7 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 40 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 40 (7 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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