Full information on isolate ERR314550 (id:27079)
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
- 27079
- isolate
- ERR314550
- alias
- SAMEA2054100
- 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
- 78
- total length
- 5,492,155 bp
- max length
- 841,290 bp
- mean length
- 70,413 bp
- N50
- 319,165
- L50
- 6
- N90
- 86,473
- L90
- 18
- N95
- 28,475
- L95
- 24
- %GC
- 57.22
- Ns
- 981
- gaps
- 10
- loci tagged
- 703
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 | 629 | 100 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 1
- num_resistance_classes
- 5
- num_resistance_genes
- 6
- Yersiniabactin
- ybt 10; ICEKp4
- YbST
- 84
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi346
- K_locus
- KL110
- K_type
- unknown (KL110)
- K_locus_confidence
- High
- K_locus_identity
- 99.06%
- K_locus_missing_genes
- KL110_16_wcpZ
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.02%
- AGly_acquired
- strA.v1^;strB.v1
- Flq_acquired
- qnrB1.v2^
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- ybtS
- 3
- ybtX
- 12
- ybtQ
- 4
- ybtP
- 3
- ybtA
- 14
- irp2
- 50
- irp1
- 274
- ybtU
- 3
- ybtT
- 15
- ybtE
- 8
- fyuA
- 2
Analysis performed: 2024-03-26; Kleborate v2.3.2
Schemes and loci
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Tools
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