Full information on isolate ERR5863522 (id:29512)
Provenance/primary metadata
- id
- 29512
- isolate
- ERR5863522
- alias
- SAMEA8664743
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 7 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Unknown
- country
- Sweden
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- blood
Sequence bin
- contigs
- 100
- total length
- 5,523,023 bp
- max length
- 444,892 bp
- mean length
- 55,231 bp
- N50
- 247,560
- L50
- 9
- N90
- 40,140
- L90
- 26
- N95
- 26,517
- L95
- 35
- %GC
- 57.13
- Ns
- 496
- gaps
- 5
- loci tagged
- 689
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 | 51 | 96 | |
| scgMLST629_S | 629 | 628 | 99 | |
Analysis
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
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- ?
- K_locus_confidence
- Good
- K_locus_identity
- 98.53%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.62%
- Bla_chr
- SHV-1
Analysis performed: 2024-03-27; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_13_0_0_0_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_13_0_0 | 7 | 1 |
| 0_0_127_13_0_0_0 | 4 | 1 |
| 0_0_127_13_0_0_0_0 | 2 | 1 |
| 0_0_127_13_0_0_0_0_0 | 1 | 1 |
| 0_0_127_13_0_0_0_0_0_0 | 0 | 1 |
| 0 | 610 | 37702 |
| 0_0 | 585 | 37702 |
| 0_0_127 | 190 | 105 |
| 0_0_127_13 | 43 | 1 |
| 0_0_127_13_0 | 10 | 1 |
| 0_0_127_13_0_0 | 7 | 1 |
| 0_0_127_13_0_0_0 | 4 | 1 |
| 0_0_127_13_0_0_0_0 | 2 | 1 |
| 0_0_127_13_0_0_0_0_0 | 1 | 1 |
| 0_0_127_13_0_0_0_0_0_0 | 0 | 1 |
Schemes and loci
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Tools
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