Full information on isolate ERR6058025 (id:59632)
Provenance/primary metadata
- id
- 59632
- isolate
- ERR6058025
- sender
- Martin Rethoret-Pasty
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 4 updates show details
- date entered
- 2024-03-29
- datestamp
- 2024-05-03
- taxonomic designation
- K. pneumoniae
- isolation year
- 2018
- city
- Blantyre
- country
- Malawi
- continent
- Africa
- source type
- Human
- host
- Human
- source details
- rectal swab
- source lab
- Queen Elizabeth Central Hospital, Blantyre, Malawi
- comments
- Lewis 2021
- accession number
- ERR6058025
Sequence bin
- contigs
- 125
- total length
- 5,546,046 bp
- max length
- 396,615 bp
- mean length
- 44,369 bp
- N50
- 123,362
- L50
- 15
- N90
- 31,521
- L90
- 47
- N95
- 21,647
- L95
- 57
- %GC
- 57.07
- Ns
- 174
- gaps
- 144
- loci tagged
- 692
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 | 626 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 1
- num_resistance_classes
- 6
- num_resistance_genes
- 12
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi27
- K_locus
- KL27
- K_type
- K27
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.96%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.56%
- AGly_acquired
- aac(3)-IId^;aac(6')-Ib-cr.v2;strA.v1^;strB.v1
- Phe_acquired
- CatB4.v1?
- Sul_acquired
- sul2
- Tet_acquired
- tet(A).v1;tet(B).v2*;tetR
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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