Full information on isolate ERR926437 (id:58963)
Projects
This isolate is a member of the following project:
- Musicha et al. 2019
- Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages (PMID: 30778540)
Provenance/primary metadata
- id
- 58963
- isolate
- ERR926437
- sender
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 3 updates show details
- date entered
- 2024-03-21
- datestamp
- 2024-03-22
- taxonomic designation
- K. pneumoniae
- isolation year
- 1996
- city
- Blantyre
- country
- Malawi
- continent
- Africa
- source type
- Human
- host
- Human
- source details
- Blood
- source lab
- Queen Elizabeth Central Hospital, Blantyre, Malawi
- comments
- Musicha 2019
- accession number
- ERR926437
Sequence bin
- contigs
- 99
- total length
- 5,767,435 bp
- max length
- 590,745 bp
- mean length
- 58,257 bp
- N50
- 210,424
- L50
- 8
- N90
- 71,094
- L90
- 27
- N95
- 36,879
- L95
- 32
- %GC
- 56.75
- Ns
- 82
- gaps
- 60
- loci tagged
- 691
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 | 625 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 3
- resistance_score
- 0
- num_resistance_classes
- 6
- num_resistance_genes
- 9
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 1 (truncated)
- AbST
- 1-1LV
- SmST
- 0
- RmST
- 0
- rmpA2
- rmpA2_8-60%
- wzi
- wzi360
- K_locus
- KL122
- K_type
- unknown (KL122)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.98%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.52%
- AGly_acquired
- aac(3)-IIa.v1;strA.v1^;strB.v1
- Phe_acquired
- catA1^
- Sul_acquired
- sul1;sul2
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA5
- Bla_acquired
- TEM-1D.v1^
- truncated_resistance_hits
- SHV-148*?-10%
- iucA
- 1
- iucB
- 1
- iucC
- 1*-44%
- iucD
- 1
- iutA
- 1
- rmpA
- 55-60%
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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Tools
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