The reference dataset for this species has substantial quality issues. Thresholds should be treated as indicative only.
Derived from 8 genomes: 4 from RefSeq and 4 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 | insufficient_data | 4 | 154,943 | 2,108 | 152,835 | 152,835 | 154,943 | 157,050 | 157,050 |
| no_of_contigs | insufficient_data | 4 | 112.5 | 5.55 | 106 | 107.5 | 113 | 118 | 118 |
| longest | insufficient_data | 4 | 464,135 | 50,697 | 413,438 | 413,438 | 464,135 | 514,832 | 514,832 |
| GC_Content | insufficient_data | 4 | 56.69 | 0 | 56.68 | 56.68 | 56.69 | 56.69 | 56.69 |
| Completeness_Specific | insufficient_data | 4 | 100 | 0 | 100 | 100 | 100 | 100 | 100 |
| Contamination | insufficient_data | 4 | 0.35 | 0.04 | 0.31 | 0.31 | 0.35 | 0.39 | 0.39 |
| Total_Coding_Sequences | insufficient_data | 4 | 5,502 | 57.5 | 5,444 | 5,444 | 5,501 | 5,559 | 5,560 |
| Genome_Size | insufficient_data | 4 | 5,773,113 | 21,773 | 5,751,340 | 5,751,340 | 5,773,058 | 5,794,831 | 5,794,997 |
Full statistics including KS test vs RefSeq and Wasserstein distance are in the downloadable summary.csv.
Derived from 8 genomes including 4 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 | 5,700,000 | 5,700,000 | 5,800,000 | 5,800,000 |
| GC_Content | 56.6 | 56.6 | 56.7 | 56.7 |
| Total_Coding_Sequences | 5,400 | 5,400 | 5,600 | 5,600 |
| Completeness_Specific | 100 | 100 | - | - |
| Contamination | - | - | 1 | 1 |
| N50 | 152,000 | 152,000 | - | - |
| no_of_contigs | - | - | 120 | 120 |
| 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 quasivariicola 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 quasivariicola 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.