Full information on isolate ERR314407 (id:27035)
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
- 27035
- isolate
- ERR314407
- alias
- SAMEA2054827
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 8 updates show details
- date entered
- 2023-02-15
- datestamp
- 2025-05-29
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 0
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- method
- Unknown
- contigs
- 187
- total length
- 5,265,976 bp
- max length
- 902,987 bp
- mean length
- 28,161 bp
- N50
- 356,188
- L50
- 5
- N90
- 89,479
- L90
- 16
- N95
- 42,562
- L95
- 19
- %GC
- 57.38
- Ns
- 1190
- gaps
- 13
- loci tagged
- 3,434
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 | |
| Kpn_cgMLST | 2752 | 2744 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 7
- num_resistance_genes
- 14
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi46
- K_locus
- KL13
- K_type
- K13
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.66%
- K_locus_missing_genes
- KL13_18_manB
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.99%
- O_locus_missing_genes
- O3b_02_manB
- AGly_acquired
- aac(3)-IId^;aac(6')-Ib-cr.v2;aadA16*;strA.v1*;strB.v1*
- Flq_acquired
- qnrB6^
- Rif_acquired
- arr-3
- Sul_acquired
- sul1;sul1;sul2
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA27
- Bla_acquired
- OXA-1*;TEM-1D.v1^
- spurious_resistance_hits
- CTX-M-103?-0%;SHV-152?-0%;SHV-187*?-42%
Analysis performed: 2024-03-26; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_348_3_0_0_0_1_0_0
- Phylogroup
- Kp1
- Sublineage
- SL1017
- Clonal group
- CG12596
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: