Full information on isolate ERR304794 (id:26861)
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
- 26861
- isolate
- ERR304794
- alias
- SAMEA1920553
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 5 updates show details
- date entered
- 2023-02-15
- datestamp
- 2023-11-27
- 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
- contigs
- 166
- total length
- 5,546,234 bp
- max length
- 920,015 bp
- mean length
- 33,412 bp
- N50
- 225,210
- L50
- 7
- N90
- 57,303
- L90
- 25
- N95
- 34,646
- L95
- 31
- %GC
- 57.27
- Ns
- 1701
- gaps
- 20
- loci tagged
- 699
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 | Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2023-04-19
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 0
- num_resistance_classes
- 3
- num_resistance_genes
- 3
- Yersiniabactin
- ybt 6; ICEKp5
- YbST
- 62
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi72
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.41%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 99.20%
- O_locus_missing_genes
- O1/O2v2_09_gmlB
- AGly_acquired
- aph3-Ia.v1*?
- Tmt_acquired
- dfrA14.v2*
- Bla_inhR_acquired
- SHV-110* +69I
- SHV_mutations
- 35Q;69I
- truncated_resistance_hits
- sul1?-0%
- ybtS
- 22
- ybtX
- 22
- ybtQ
- 6
- ybtP
- 24
- ybtA
- 16
- irp2
- 53
- irp1
- 266
- ybtU
- 9
- ybtT
- 17
- ybtE
- 5
- fyuA
- 30
Analysis performed: 2024-03-27; Kleborate v2.3.2
Schemes and loci
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Tools
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