Full information on isolate ERR971967 (id:58983)
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
- 58983
- isolate
- ERR971967
- 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
- 2007
- 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
- ERR971967
Sequence bin
- contigs
- 135
- total length
- 5,478,238 bp
- max length
- 929,402 bp
- mean length
- 40,580 bp
- N50
- 177,743
- L50
- 10
- N90
- 35,292
- L90
- 33
- N95
- 21,028
- L95
- 43
- %GC
- 57.14
- Ns
- 174
- gaps
- 151
- loci tagged
- 690
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 | 628 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 6
- num_resistance_genes
- 9
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi202
- K_locus
- KL127
- K_type
- unknown (KL127)
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 97.88%
- K_locus_missing_genes
- KL127_10,KL127_16_rmlA,KL127_18_rmlC
- O_locus
- OL101
- O_type
- unknown (OL101)
- O_locus_problems
- ?-+*
- O_locus_confidence
- Good
- O_locus_identity
- 92.04%
- O_locus_missing_genes
- OL101_02_rfbA,OL101_04_rfbC
- AGly_acquired
- aac(3)-IIa.v1;strA.v1;strB.v1
- MLS_acquired
- mphA
- Phe_acquired
- catA1*
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA5
- Bla_acquired
- SCO-1;TEM-1D.v1^
- spurious_resistance_hits
- SHV-100*?-36%;SHV-12*?-0%
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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Tools
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