Summary
Downloadable tables of QualiBact thresholds and reference distributions across every species, derived from each species' preferred QC scheme. The quality criteria table below is the primary dataset; the other tables describe the reference distributions those thresholds were fit from. For programmatic access see the API endpoints section.
Quality criteria
Per-species, per-metric quality thresholds. Each row gives four boundaries: Fail below and Fail above are the published cut-offs that downstream tools consume; Warn below and Warn above are the tighter inner boundaries derived from the reference distribution. A value inside the warn range passes, between warn and fail it warns, and outside fail it fails. This is the same data the per-species pages render.
Species⇅ | Scheme⇅ | Engine flag⇅ | Metric⇅ | Fail below⇅ | Warn below⇅ | Warn above⇅ | Fail above⇅ |
|---|---|---|---|---|---|---|---|
| Achromobacter xylosoxidans | qualibact-v1.0 | Genome_Size | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | GC_Content | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | Total_Coding_Sequences | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | Completeness_Specific | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | Contamination | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | N50 | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | no_of_contigs | |||||
| Achromobacter xylosoxidans | qualibact-v1.0 | longest | |||||
| Achromobacter xylosoxidans | qualibact-v1.1 | Genome_Size | |||||
| Achromobacter xylosoxidans | qualibact-v1.1 | GC_Content |
Summary statistics
Per-metric distribution statistics for each species (preferred QC scheme only). The preview below shows the most useful columns; the full CSV also includes RefSeq comparison statistics (KS test, Wasserstein distance) and pre-filter bounds. Useful for building your own thresholds or diagnosing how a candidate assembly sits within the reference distribution.
Species⇅ | Metric⇅ | n⇅ | Mean⇅ | Median⇅ | SD⇅ | Q1⇅ | Q3⇅ | RefSeq n⇅ |
|---|---|---|---|---|---|---|---|---|
| Achromobacter xylosoxidans | N50 | 286 | 243,388 | 144,313 | 200,292 | 98,766 | 373,713 | 0 |
| Achromobacter xylosoxidans | number | 286 | 116.8497 | 104 | 79.9994 | 60 | 141.75 | 0 |
| Achromobacter xylosoxidans | longest | 286 | 665,754 | 458,029 | 484,258 | 303,881 | 949,279 | 0 |
| Achromobacter xylosoxidans | GC_Content | 286 | 67.6077 | 67.6141 | 0.1684 | 67.5003 | 67.7343 | 28 |
| Achromobacter xylosoxidans | Completeness_Specific | 286 | 99.9999 | 100 | 0.0012 | 100 | 100 | 28 |
| Achromobacter xylosoxidans | Contamination | 286 | 0.3159 | 0.18 | 0.4446 | 0.1 | 0.34 | 28 |
| Achromobacter xylosoxidans | Total_Coding_Sequences | 286 | 6,081 | 6,080 | 201.1871 | 5,904 | 6,241 | 28 |
| Achromobacter xylosoxidans | Genome_Size | 286 | 6,634,277 | 6,615,944 | 189,645 | 6,479,491 | 6,790,041 | 28 |
| Achromobacter xylosoxidans | N50 | 387 | 323,578 | 151,927 | 320,676 | 67,362 | 503,574 | 0 |
| Achromobacter xylosoxidans | number | 387 | 100.9587 | 78 | 85.5554 | 31 | 150 | 0 |
Species count summary
Per species: how many reference genomes contributed to the thresholds (split between RefSeq and other sources), the engine's quality flag for that reference dataset, and how the published thresholds partition the broader All-The-Bacteria dataset into PASS / WARN / FAIL tiers. Use this to sanity-check thresholds for species with small reference sets or non-PASS engine flags.
Species⇅ | Scheme⇅ | Engine flag⇅ | Total genomes⇅ | Other sources⇅ | RefSeq⇅ | PASS⇅ | WARN⇅ | FAIL⇅ |
|---|---|---|---|---|---|---|---|---|
| Achromobacter xylosoxidans | qualibact-v1.1 | 415 | 387 | 28 | ||||
| Acinetobacter baumannii | qualibact-v1.0 | 27,262 | 26,247 | 1,015 | ||||
| Acinetobacter baylyi | qualibact-v1.0 | 245 | 242 | 3 | ||||
| Acinetobacter johnsonii | qualibact-v1.0 | 112 | 87 | 25 | ||||
| Acinetobacter nosocomialis | qualibact-v1.0 | 356 | 321 | 35 | ||||
| Acinetobacter pittii | qualibact-v1.0 | 674 | 592 | 82 | ||||
| Acinetobacter radioresistens | qualibact-v1.0 | 97 | 90 | 7 | ||||
| Acinetobacter ursingii | qualibact-v1.0 | 115 | 107 | 8 | ||||
| Actinobacillus lignieresii | qualibact-v1.0 | 482 | 481 | 1 | ||||
| Aerococcus urinae | qualibact-v1.0 | 100 | 95 | 5 |
API endpoints
QualiBact ships a small set of versioned static endpoints under /api/v2/ so that downstream tools can fetch thresholds without scraping HTML. These files are regenerated on every site build from the per-species manifests. Third-party comparison schemes that QualiBact does not publish itself (currently EnteroBase) live under /api/v2/external/ in the same shape — kept separate so the canonical /api/v2/ contract only carries QualiBact-published thresholds.
| Endpoint | What it is |
|---|---|
| /api/v2/thresholds.csv | Long-form CSV: one row per (species, scheme, metric) with fail/warn lower & upper bounds. The source for the table above. |
| /api/v2/thresholds.json | Same data as the CSV but JSON-keyed and grouped, easier for programmatic consumption. |
| /api/v2/index.json | Manifest: schema version, generation timestamp, list of available species and the endpoint paths. |
| /static/species/{species}/{scheme}/manifest.json | Per-species, per-scheme bundle: thresholds, distribution summary, plot URLs, and warning flags. One file per pair — the same one the per-species pages read. |
External / third-party comparison schemes
Same shape as the canonical endpoints above, but for schemes QualiBact does not publish itself. Currently carries EnteroBase (enterobase-v2.3) rows.
| Endpoint | What it is |
|---|---|
| /api/v2/external/thresholds.csv | Long-form CSV of third-party comparison thresholds, mirroring the canonical CSV shape. |
| /api/v2/external/thresholds.json | Same data as the external CSV, JSON-keyed and grouped by species & scheme for programmatic consumption. |
| /api/v2/external/index.json | Manifest for the external endpoints: schema version, generation timestamp, species count, and the list of species covered. |
The path prefix v2 means the schema will not break compatibly. A schema change that does break consumers gets a new prefix (v3) and v2 stays in place until usage drops.