Full information on isolate ERR314466 (id:27040)
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
- 27040
- isolate
- ERR314466
- alias
- SAMEA2054047
- 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
- 2012
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 30
- total length
- 5,244,261 bp
- max length
- 624,947 bp
- mean length
- 174,809 bp
- N50
- 485,446
- L50
- 5
- N90
- 142,202
- L90
- 13
- N95
- 66,473
- L95
- 16
- %GC
- 57.54
- Ns
- 1379
- gaps
- 14
- loci tagged
- 701
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 | 628 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 1
- num_resistance_classes
- 6
- num_resistance_genes
- 9
- Yersiniabactin
- ybt 9; ICEKp3
- YbST
- 189
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi62
- K_locus
- KL62
- K_type
- K62
- K_locus_confidence
- High
- K_locus_identity
- 99.72%
- K_locus_missing_genes
- KL62_12
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 97.87%
- AGly_acquired
- aadA2^;aph3-Ia.v1^;strA.v1^;strB.v1
- MLS_acquired
- mphA
- Sul_acquired
- sul1;sul2^
- Tmt_acquired
- dfrA12
- Bla_ESBL_acquired
- CTX-M-14^
- Bla_chr
- SHV-172*
- SHV_mutations
- 35Q
- Flq_mutations
- GyrA-83Y
- ybtS
- 5
- ybtX
- 11
- ybtQ
- 6
- ybtP
- 5
- ybtA
- 1
- irp2
- 254
- irp1
- 15
- ybtU
- 9
- ybtT
- 5
- ybtE
- 5
- fyuA
- 25
Analysis performed: 2024-03-26; Kleborate v2.3.2
Schemes and loci
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Tools
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Analysis: