Full information on isolate ERR314403 (id:26766)
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
- 26766
- isolate
- ERR314403
- alias
- SAMEA2053998
- 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
- 0
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- method
- Unknown
- contigs
- 409
- total length
- 5,553,763 bp
- max length
- 1,315,780 bp
- mean length
- 13,579 bp
- N50
- 355,689
- L50
- 5
- N90
- 64,446
- L90
- 16
- N95
- 7,307
- L95
- 30
- %GC
- 57.16
- Ns
- 1112
- gaps
- 14
- 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
- 2
- num_resistance_genes
- 3
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi383
- K_locus
- KL102
- K_type
- unknown (KL102)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.25%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.45%
- AGly_acquired
- strA.v1;strB.v1
- Tet_acquired
- tet(A).v1
- 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_220_7_25_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL152
- Clonal group
- CG105
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_220_7_25_0 | 7 | 1 |
| 0_0_220_7_25_0_0 | 4 | 1 |
| 0_0_220_7_25_0_0_0 | 2 | 1 |
| 0_0_220_7_25_0_0_0_0 | 1 | 1 |
| 0_0_220_7_25_0_0_0_0_0 | 0 | 1 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_220 | 190 | 221 |
| 0_0_220_7 | 43 | 52 |
| 0_0_220_7_25 | 10 | 1 |
| 0_0_220_7_25_0 | 7 | 1 |
| 0_0_220_7_25_0_0 | 4 | 1 |
| 0_0_220_7_25_0_0_0 | 2 | 1 |
| 0_0_220_7_25_0_0_0_0 | 1 | 1 |
| 0_0_220_7_25_0_0_0_0_0 | 0 | 1 |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: