Full information on isolate ERR2303394 (id:27354)
Provenance/primary metadata
- id
- 27354
- isolate
- ERR2303394
- aliases
- 7; SAMEA104590234
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 7 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2014
- city
- Unknown
- country
- Cambodia
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Swab
Sequence bin
- contigs
- 120
- total length
- 5,722,982 bp
- max length
- 369,744 bp
- mean length
- 47,692 bp
- N50
- 135,110
- L50
- 14
- N90
- 30,292
- L90
- 47
- N95
- 18,927
- L95
- 59
- %GC
- 56.76
- Ns
- 203
- gaps
- 3
- 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 | 627 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 1
- num_resistance_classes
- 9
- num_resistance_genes
- 11
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- unknown (KL7)
- K_type
- unknown (K7)
- K_locus_problems
- ?-
- K_locus_confidence
- Low
- K_locus_identity
- 98.46%
- K_locus_missing_genes
- KL7_08_wckC,KL7_10_wzy,KL7_12_wclS
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.61%
- AGly_acquired
- aac(6')-Ib-cr.v2;aadA16*
- Flq_acquired
- qnrB6^
- MLS_acquired
- mphA
- Rif_acquired
- arr-3
- Sul_acquired
- sul1;sul1
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA27
- Bla_acquired
- TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1
Analysis performed: 2024-03-26; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_10_4_0_0_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_10_4_0 | 7 | 4 |
| 0_0_127_10_4_0_0 | 4 | 4 |
| 0_0_127_10_4_0_0_0 | 2 | 4 |
| 0_0_127_10_4_0_0_0_0 | 1 | 4 |
| 0_0_127_10_4_0_0_0_0_0 | 0 | 4 |
| 0 | 610 | 37702 |
| 0_0 | 585 | 37702 |
| 0_0_127 | 190 | 105 |
| 0_0_127_10 | 43 | 20 |
| 0_0_127_10_4 | 10 | 4 |
| 0_0_127_10_4_0 | 7 | 4 |
| 0_0_127_10_4_0_0 | 4 | 4 |
| 0_0_127_10_4_0_0_0 | 2 | 4 |
| 0_0_127_10_4_0_0_0_0 | 1 | 4 |
| 0_0_127_10_4_0_0_0_0_0 | 0 | 4 |
Schemes and loci
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Tools
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