Full information on isolate CGMHP0539-1 (id:75259)
Provenance/primary metadata
- id
- 75259
- isolate
- CGMHP0539-1
- sender
- Yu Yang, Zhejiang Chinese Medical University
- curator
- Auto Tagger
- update history
- 4 updates show details
- date entered
- 2024-12-30
- datestamp
- 2026-03-14
- taxonomic designation
- K. pneumoniae
- isolation year
- 2024
- city
- Hangzhou
- country
- China
- continent
- Asia
- source type
- Human
- host
- human
- source details
- stool
- infection
- carriage
- other source info
- feces
Sequence bin
- method
- Illumina
- contigs
- 182
- total length
- 5,358,936 bp
- max length
- 587,930 bp
- mean length
- 29,445 bp
- N50
- 195,730
- L50
- 8
- N90
- 45,642
- L90
- 31
- N95
- 21,457
- L95
- 39
- %GC
- 57.41
- Ns
- 0
- gaps
- 0
- loci tagged
- 693
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
Kaptive
| Database | Best match locus | Best match type | Match confidence | Problems | Identity | Coverage | Length discrepancy | Expected genes in locus | Missing expected genes | Other genes in locus | Other genes in locus, details | Expected genes outside locus | Expected genes outside locus, details | Other genes outside locus | Other genes outside locus, details | Truncated genes, details | Extra genes, details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Klebsiella K locus | KL170 | unknown (KL170) | Typeable | ?3! | 98.57% | 99.82% | n/a | 23 / 23 (100.00%) | 0 | 0 / 23 (0.00%) | 7 | KL40_03_wcpO,98.98%,99.80%;KL40_04,99.50%,100.00%;KL40_05_rfaG,99.47%,100.00%;KL150_19_gmd,99.10%,100.00%;KL101_14_wzx,98.13%,24.43%,partial;KL28_15_wcaJ,100.00%,9.72%,partial;KL28_14_wbaZ,100.00%,7.55%,partial | KL170_13_wcqP,99.60%,92.16%,truncated;KL170_17,100.00%,82.14%,truncated | ||||
| Klebsiella O locus | OL2α.2 | O1αβ,2β | Typeable | 99.07% | 100.00% | 0 bp | 7 / 7 (100.00%) | 0 | 0 / 7 (0.00%) | 4 | OL12_01_rfbB,98.02%,99.72%;OL13_03_rfbD,98.31%,100.00%;OL13_02_rfbA,98.96%,100.00%;OL13_04_rfbC,96.69%,98.37% | Extra_genes_wbbYZ_02_wbbY,99.73%,100.00%;Extra_genes_gml2β_03_gmlC,97.12%,100.00%;Extra_genes_gml2β_02_gmlB,99.08%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.26%,100.00%;Extra_genes_gml2β_01_gmlA,100.00%,100.00% |
Klebsiella K locus
Klebsiella O locus
Analysis performed: 2026-03-24; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 0
- Bla_chr
- SHV-1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Ciprofloxacin_prediction
- wildtype S
- Ciprofloxacin_profile_support
- 90.99% S (N=5168/5680)
- Ciprofloxacin_profile
- 0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
- Ciprofloxacin_MIC_prediction
- 0.25 mg/L [0.25-0.25]
- K_locus
- KL170
- K_type
- unknown (KL170)
- K_locus_confidence
- Typeable
- K_locus_problems
- ?3!
- K_locus_identity
- 98.57%
- O_locus
- OL2α.2
- O_type
- O1αβ,2β
- O_locus_confidence
- Typeable
- O_locus_identity
- 99.07%
Analysis performed: 2026-01-16; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_1_4_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL6
- Clonal group
- CG10015
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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