Klebsiella pasteurii is a Gram-negative, non-motile rod of the family Enterobacteriaceae, recently delineated as a novel species within the Klebsiella oxytoca species complex. It has been recovered from both clinical and environmental sources and is frequently misidentified as K. oxytoca by routine phenotypic methods. Genomic analyses place K. pasteurii as a distinct clade, and certain strains harbour genes encoding cytotoxin production and antimicrobial resistance.
The reference dataset for this species has substantial quality issues. Thresholds should be treated as indicative only.
Derived from 36 genomes: 18 from RefSeq and 18 from other sources. For the derivation pipeline and the PASS / WARN / FAIL verdict model, see the methods page for REFSEQ-QC-v1.
This table summarises the distribution of each metric, including standard deviation, mean, median, and percentiles.
A combined summary table across all species is available on the summary page.
| Metric | Distribution | n | Mean | SD | Min | Q1 | Median | Q3 | Max |
|---|---|---|---|---|---|---|---|---|---|
| N50 | normal | 18 | 343,702 | 95,660 | 216,678 | 223,549 | 394,313 | 405,588 | 489,082 |
| no_of_contigs | normal | 18 | 63.78 | 21.46 | 42 | 46 | 53 | 78 | 109 |
| longest | normal | 18 | 806,555 | 312,481 | 474,932 | 609,421 | 660,910 | 888,367 | 1,456,430 |
| GC_Content | normal | 18 | 55.25 | 0.14 | 54.95 | 55.17 | 55.28 | 55.34 | 55.45 |
| Completeness_Specific | non-normal | 18 | 100 | 0 | 100 | 100 | 100 | 100 | 100 |
| Contamination | non-normal | 18 | 0.67 | 0.58 | 0.23 | 0.27 | 0.43 | 0.53 | 1.85 |
| Total_Coding_Sequences | normal | 18 | 5,743 | 236.73 | 5,388 | 5,632 | 5,809 | 5,867 | 6,196 |
| Genome_Size | normal | 18 | 6,147,419 | 197,429 | 5,845,210 | 6,061,825 | 6,213,402 | 6,249,744 | 6,497,593 |
Full statistics including KS test vs RefSeq and Wasserstein distance are in the downloadable summary.csv.
Derived from 36 genomes including 18 RefSeq references
Both Fail and Warn bands shown as the published rounded values — easier to cite and consistent across the species page, CSV downloads, and downstream QC tools.
| Metric | Fail below | Warn below | Warn above | Fail above |
|---|---|---|---|---|
| Genome_Size | 5,800,000 | 5,800,000 | 6,500,000 | 6,500,000 |
| GC_Content | 54.9 | 54.9 | 55.5 | 55.5 |
| Total_Coding_Sequences | 5,300 | 5,300 | 6,200 | 6,200 |
| Completeness_Specific | 100 | 100 | - | - |
| Contamination | - | - | 2 | 2 |
| N50 | 216,000 | 216,000 | - | - |
| no_of_contigs | - | - | 110 | 110 |
| longest | - | - | - | - |
How to read this: a value between the two warn columns is typical for this species and passes QC. A value between a warn column and the corresponding fail column is borderline — worth a manual look but not an outright failure. A value outside the fail columns is unusual enough to fail QC.
This plot shows the relationship between the number of coding sequences (CDS) and genome size — how the number of genes scales with assembly length. The relationship should be roughly linear: as genome size increases, the number of coding sequences should rise proportionally. A secondary trend line or non-linear behaviour can indicate either bona fide sub-populations within the retained genomes (e.g. distinct sub-clades) or residual contamination that survived filtering.
Histogram comparing SRA to RefSeq; each bar shows genome density across value ranges to highlight shifts, peaks, or outliers.
QQ (quantile-quantile) plot comparing SRA and RefSeq. Points along the diagonal follow the expected distribution; deviations indicate skew, outliers, or other systematic differences.
A table of complete RefSeq genomes for Klebsiella pasteurii used to calibrate this scheme. The file includes accessions, some sample information, genome size, GC content, and other key metrics.
Per-assembly inputs the engine used to derive the Klebsiella pasteurii reference distribution for this scheme: sample, sylph species call, N50, contig count, longest contig, total length, completeness, contamination, total coding sequences, genome size, GC content. Gzipped CSV.