Full information on isolate ERR304799 (id:26872)
Projects
This isolate is a member of the following project:
- Ellington et al. 2019
- Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center (https://doi.org/10.1186/s13059-019-1785-1)
Provenance/primary metadata
- id
- 26872
- isolate
- ERR304799
- alias
- SAMEA1920560
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 6 updates show details
- date entered
- 2023-02-15
- datestamp
- 2023-11-27
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2011
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 96
- total length
- 5,398,721 bp
- max length
- 627,937 bp
- mean length
- 56,237 bp
- N50
- 225,796
- L50
- 9
- N90
- 54,815
- L90
- 29
- N95
- 26,218
- L95
- 36
- %GC
- 57.38
- Ns
- 1081
- gaps
- 11
- loci tagged
- 699
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
- 1
- resistance_score
- 0
- num_resistance_classes
- 4
- num_resistance_genes
- 8
- Yersiniabactin
- ybt 14; ICEKp5?
- YbST
- 131
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi141
- K_locus
- KL25
- K_type
- K25
- K_locus_confidence
- High
- K_locus_identity
- 99.16%
- K_locus_missing_genes
- KL25_09_wfeD
- O_locus
- O5
- O_type
- O5
- O_locus_problems
- ?-*
- O_locus_confidence
- Good
- O_locus_identity
- 94.20%
- O_locus_missing_genes
- O5_03_wzm
- AGly_acquired
- aadA1.v1^;aph3-Ia.v1^;strA.v1^;strB.v1
- Sul_acquired
- sul1;sul2*
- Tmt_acquired
- dfrA1.v2
- Bla_acquired
- TEM-1D.v1^
- truncated_resistance_hits
- SHV-143*?-0%
- ybtS
- 4
- ybtX
- 111
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 247
- irp1
- 184
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
Analysis performed: 2024-03-27; Kleborate v2.3.2
Schemes and loci
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Tools
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