Protocol

Base-resolution RNA-seq prediction (AlphaGenome paper)

Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

2 evaluations · 4 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Dataset and biological context	Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Split	Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Allowed inputs and adaptation	Reference sequence; the additional AlphaGenome RNA-seq head and unscaled Borzoi predictions repeated across each original 32-bp bin. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Metrics as reported	Track @1bp (log1p scale pearsonr); Track @1bp (normal scale pearsonr) Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Aggregation	Pearson correlation; genome-track methods average individual track correlations for assay groups. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Uncertainty	Not reported for these summary-table scores. · Not reported in inspected sources Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

How it worksBase-resolution RNA-seq prediction: evaluation procedure

Conceptual summary of the cited procedure; model-specific conditions are given below.

Sources (3)

What is tested

Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?

Sources (3)

Procedure

Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.

Sources (3)

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

Base-resolution RNA-seq prediction (AlphaGenome paper)

Track @1bp (normal scale pearsonr) (correlation) · Higher values are better for this metric.

Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?

Evaluation protocol · Base-resolution RNA-seq prediction: evaluated data subset

Borzoi (paper Table 3) · Configuration · Author-reported evaluation0.460
AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head · Configuration · Author-reported evaluation0.59

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10; 'Suppl Table 3 Track performance'!K10

Values, uncertainty and evidence

Track @1bp (normal scale pearsonr): original source values
Tested entity	Printed value	Uncertainty	Evidence
Borzoi (paper Table 3) · Configuration	0.460 correlation	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10
AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head · Configuration	0.59 correlation	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K10

Scope and limitations

This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.
Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.
Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 2 evaluations · 4 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
Borzoi (paper Table 3): Base-resolution RNA-seq prediction Configuration: Borzoi (paper Table 3)Protocol: Base-resolution RNA-seq prediction (AlphaGenome paper)Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Author-reported evaluation · Evaluation metadata: needs review
0.460 Track @1bp (normal scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10 Source checking is not independent reproduction.
0.750 Track @1bp (log1p scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J11 Source checking is not independent reproduction.
AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: Base-resolution RNA-seq prediction Configuration: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq headProtocol: Base-resolution RNA-seq prediction (AlphaGenome paper)Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Author-reported evaluation · Evaluation metadata: needs review
0.80 Track @1bp (log1p scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K11 Source checking is not independent reproduction.
0.59 Track @1bp (normal scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K10 Source checking is not independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.

Paper or primary resource	Version	Reference
alphagenome: Journal full-text XML	Retrieved page snapshot; no immutable publisher revision supplied	Read source
AlphaGenome Nature 2026 supplementary comparison tables	Nature version of record, 28 January 2026	Read source DOI: 10.1038/s41586-025-10014-0
AlphaGenome Nature 2026 supplementary methods	Supplement to Nature version of record, 28 January 2026; content hash pinned	Read source

What is still missing

Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.
Subsequent studies use different datasets and are not pooled with this paper.

Search and extraction details

complete comparison extracted

Searches

AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction
AlphaGenome independent evaluation benchmark 2026 variant effects

Evidence locations

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

Upsampled Borzoi output has no new sub-bin information; normal-scale gains partly reflect exon-boundary resolution. The paper restricts inclusion to tracks meeting its data-concordance check.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

Profile review details

Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.

Stable record: alphagenome-2026-t3-protocol-5

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.

42 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram steps ["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"] Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"] Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram steps ["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"] Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram title Base-resolution RNA-seq prediction: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Base-resolution RNA-seq prediction: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram title Base-resolution RNA-seq prediction: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Dataset and biological context Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release history

AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-t3-protocol-5

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 5
source table: 3
reference levels: metric: Track @1bp (normal scale pearsonr); printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H10; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: Track @1bp (log1p scale pearsonr); printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H11; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
comparison panels: id: paper-figure-8386b0541f037485a4; title: Base-resolution RNA-seq prediction (AlphaGenome paper); protocol id: alphagenome-2026-t3-protocol-5; dataset id: alphagenome-2026-t3-dataset-5; metric: Track @1bp (normal scale pearsonr); unit: correlation; direction: higher; result ids: alphagenome-2026-result-79a4f4e2e0c4b236; alphagenome-2026-result-9f00e9eb53838702; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 3 Track performance'!J10; 'Suppl Table 3 Track performance'!K10; context: Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?; caveats: This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.; Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.; Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.; review: method: automated_source_review; date: 2026-09-17; id: paper-figure-bc86ad58ab38b5c81b; title: Base-resolution RNA-seq prediction (AlphaGenome paper); protocol id: alphagenome-2026-t3-protocol-5; dataset id: alphagenome-2026-t3-dataset-5; metric: Track @1bp (log1p scale pearsonr); unit: correlation; direction: higher; result ids: alphagenome-2026-result-8afbbf27535ee23d; alphagenome-2026-result-f84062873874488e; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 3 Track performance'!K11; 'Suppl Table 3 Track performance'!J11; context: Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?; caveats: This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.; Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.; Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_comparison_extracted; primary sources: evidence-official-56e5abfb5f12f1cd3b20; source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; inspected locators: 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training; searched queries: AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction; AlphaGenome independent evaluation benchmark 2026 variant effects; gaps: Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.; Subsequent studies use different datasets and are not pooled with this paper.; claim scope: Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training; ambiguities: None recorded

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