Full information on isolate ERR971959 (id:58978)
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
- 58978
- isolate
- ERR971959
- 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
- 2004
- 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
- ERR971959
Sequence bin
- contigs
- 125
- total length
- 5,870,115 bp
- max length
- 446,616 bp
- mean length
- 46,961 bp
- N50
- 176,024
- L50
- 11
- N90
- 45,493
- L90
- 35
- N95
- 20,230
- L95
- 44
- %GC
- 56.63
- Ns
- 123
- gaps
- 91
- loci tagged
- 695
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
- 3
- resistance_score
- 0
- num_resistance_classes
- 6
- num_resistance_genes
- 8
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 1-1LV
- SmST
- 0
- RmST
- 0
- rmpA2
- rmpA2_8-60%
- wzi
- wzi2
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.75%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.97%
- AGly_acquired
- aac(3)-IIa.v1;aadA4.v1*;strB.v1
- Phe_acquired
- catA1^
- Sul_acquired
- sul2*
- Tet_acquired
- tet(D)*
- Tmt_acquired
- dfrA21*
- Bla_acquired
- TEM-1D.v1^
- truncated_resistance_hits
- SHV-28.v1*?-0%;strA.v1*-3%
- iucA
- 1
- iucB
- 1
- iucC
- 1*
- 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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