Full information on isolate ERR304788 (id:26828)
Projects
This isolate is a member of the following project:
- Ellington et al. 2019
- Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center (https://doi.org/10.1186/s13059-019-1785-1)
Provenance/primary metadata
- id
- 26828
- isolate
- ERR304788
- alias
- SAMEA1920548
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 6 updates show details
- date entered
- 2023-02-15
- datestamp
- 2023-11-27
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2007
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 40
- total length
- 5,274,417 bp
- max length
- 732,159 bp
- mean length
- 131,861 bp
- N50
- 407,643
- L50
- 5
- N90
- 120,379
- L90
- 14
- N95
- 86,541
- L95
- 17
- %GC
- 57.42
- Ns
- 1281
- gaps
- 13
- loci tagged
- 690
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
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 4
- num_resistance_genes
- 4
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi260
- K_locus
- KL20
- K_type
- K20
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.89%
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.52%
- AGly_acquired
- aadA*
- Sul_acquired
- sul1
- Tet_acquired
- tet(A).v1
- Bla_acquired
- OXA-1
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
Analysis performed: 2024-03-27; Kleborate v2.3.2
Schemes and loci
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Tools
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Analysis: