Full information on isolate ERR311562 (id:25196)
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
- 25196
- isolate
- ERR311562
- alias
- SAMEA2053995
- 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
- 1800
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- human
- source details
- Unknown
Sequence bin
- contigs
- 66
- total length
- 5,375,619 bp
- max length
- 466,837 bp
- mean length
- 81,449 bp
- N50
- 284,837
- L50
- 8
- N90
- 56,325
- L90
- 24
- N95
- 43,134
- L95
- 29
- %GC
- 57.27
- Ns
- 987
- gaps
- 10
- loci tagged
- 705
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
- 7
- num_resistance_genes
- 10
- Yersiniabactin
- ybt 10; ICEKp4
- YbST
- 17
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi93
- K_locus
- KL112
- K_type
- unknown (KL112)
- K_locus_problems
- ?
- K_locus_confidence
- Good
- K_locus_identity
- 98.65%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.52%
- AGly_acquired
- aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;strA.v1^;strB.v1
- Phe_acquired
- CatB4.v1?
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-28.v1^
- Flq_mutations
- GyrA-83F;GyrA-87A;ParC-80I
- ybtS
- 15
- ybtX
- 3
- ybtQ
- 4
- ybtP
- 3
- ybtA
- 3
- irp2
- 7
- irp1
- 28
- ybtU
- 3
- ybtT
- 3
- ybtE
- 3
- fyuA
- 3
Analysis performed: 2024-03-26; Kleborate v2.3.2
Schemes and loci
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Tools
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