Average precision (DNM1 minigene screen, active vs inactive variants) of CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1) on DNM1 intron saturation mutagenesis minigene splicing screen (AlphaGenome Atlas Data S1)
0.289 Average precision (DNM1 minigene screen, active vs inactive variants)
Methods
- Tested configuration
- CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)
- Protocol
- DNM1 minigene screen, active versus inactive variants, average precision (AlphaGenome Atlas)
- Dataset
- DNM1 intron saturation mutagenesis minigene splicing screen (AlphaGenome Atlas Data S1)
- Procedure
- DNM1 minigene screen, active versus inactive variants, average precision (AlphaGenome Atlas)
- Evaluation
- CADD PHRED on the DNM1 minigene splicing screen (AlphaGenome Atlas fig. S9E)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedAlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S9E legend entry 'CADD PHRED (AP=0.289)' (page 60)
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- None; prospective experimental screen
- Adaptation
- None
- Scoring implementation
- Average precision (legend 'AP'; text 'AUPRC')
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.289 Individual claims | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) fig. S9E legend entry 'CADD PHRED (AP=0.289)' (page 60) Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | source checked ["source-hash-verification","independent-cell-check","automated-source-review"] · 2026-11-01 author reported Audit detailsChecked that the value is printed inside the quoted sentence or legend entry and that the quote occurs in the pdftotext text of a 2026-11-01 retrieval; rare-disease recalls read against the paragraph on page 7. The 2026-11-01 retrieval is stamped differently from the pinned bytes (different SHA-256); re-running the extractor on it, with only the hash assertion relaxed, reproduced batch.jsonl byte for byte. Verdict in docs/reviews/2026-11-01-alphagenome-atlas-lu-brandes.md. Field: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. Extraction artifact SHA-256: |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages)
Technical metadata and extraction receipts
Stable ID: ag-atlas-20261019-result-dnm1-cadd-v1-7-ap
- metric
- average-precision
- metric direction
- higher
- unit
- unitless
- printed value
- 0.289
- numeric value
- 0.289
- metric qualifier
- DNM1 minigene screen, active vs inactive variants
- source locator
- fig. S9E legend entry 'CADD PHRED (AP=0.289)' (page 60)
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; independent-cell-check; automated-source-review; method note: Legend string asserted as an exact substring of the pdftotext -layout text; values also asserted against the Results prose where it names them.; reviewer: claude; reviewer note: Independent Claude review agent for PR #214, 2026-11-01; did not extract this batch; no human review claimed.; date: 2026-11-01; artifact sha256: b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453; retrieval url: https://www.medrxiv.org/content/10.64898/2026.09.16.26363192v1.full.pdf; note: Checked that the value is printed inside the quoted sentence or legend entry and that the quote occurs in the pdftotext text of a 2026-11-01 retrieval; rare-disease recalls read against the paragraph on page 7. The 2026-11-01 retrieval is stamped differently from the pinned bytes (different SHA-256); re-running the extractor on it, with only the hash assertion relaxed, reproduced batch.jsonl byte for byte. Verdict in docs/reviews/2026-11-01-alphagenome-atlas-lu-brandes.md.