Evidence claim

Alavi 2026 AlphaGenome splicing discrepancy: corrected values added from the revised preprint

Evidence concern: excluded from comparisons

The AlphaGenome rows of Tables III, IV and the extended OPA1 positive calls come from scripts that pass a 0-based position to AlphaGenome's 1-based genome.Variant, so each variant was applied one base from its true position. The author labelled the report a bug on 2026-10-20 and said rerunning with the 1-based position substantially improved accuracy. The AlphaGenome results are disputed until the rerun is published; the other models' rows are not affected.Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III and Table IV, rows 'ALPHAGENOME (SPLICE SCORER)', 'ALPHAGENOME (JUNCTION SCORER)' and 'ALPHAGENOME (EITHER MODULE)'; scripts 2c8_alphagenome_splicescorer.py lines 98 and 120 and 2c8_alphagenome_junctionscorer.py lines 89 and 110 at commit 3c0c6cc; https://github.com/marcel-2c8/Probing-genomic-foundation-models-2026/issues/2

Discrepancy review of AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)

confirmed-error

Version 2 of Alavi 2026 reruns AlphaGenome with the coordinate fix. Its 56 AlphaGenome results are added; 28 of them rerun a version 1 scorer and replace its disputed results.

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.

111 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Action corrected-records Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.action` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Action corrected-records Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 pages) Retrieved: 2026-11-01T14:45:27Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.action` Source artifact SHA-256: `07bd32fffc1b31c222d43b0b18c213928e3fe111cc71c02fe2f95e64e6f7a798` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. Inspected artifact
Action corrected-records Context-only references	Alavi 2026 AlphaGenome scoring scripts at commit 2a3875de (marcel-2c8/splicing-model-eval-2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: marcel-2c8/splicing-model-eval-2026 commit 2a3875de6635d3c9b51c71c8018d23df0df98d37 (2026-10-31) Retrieved: 2026-11-01T14:48:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.action` Source artifact SHA-256: `84b4887ca3b44a6600d6a02046ab6de9d2f78c49592f82b16221d32fa5160516` Hash scope: SHA-256 of 2c8_alphagenome_merged_splicing_scorer.py at the commit. The other two scripts at the same commit: 2c8_alphagenome_splicescorer.py 0c425043d31e02b1ca6fe0ce1120051352a0b2eae2571e70ce4f05f14114c151, 2c8_alphagenome_junctionscorer.py 9f260b27b06670505a903e8695ce020ac7432acd640a7041823d47c762bfbcec. Inspected artifact
Date 2026-11-01 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.date` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Date 2026-11-01 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 pages) Retrieved: 2026-11-01T14:45:27Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.date` Source artifact SHA-256: `07bd32fffc1b31c222d43b0b18c213928e3fe111cc71c02fe2f95e64e6f7a798` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. Inspected artifact
Date 2026-11-01 Context-only references	Alavi 2026 AlphaGenome scoring scripts at commit 2a3875de (marcel-2c8/splicing-model-eval-2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: marcel-2c8/splicing-model-eval-2026 commit 2a3875de6635d3c9b51c71c8018d23df0df98d37 (2026-10-31) Retrieved: 2026-11-01T14:48:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.date` Source artifact SHA-256: `84b4887ca3b44a6600d6a02046ab6de9d2f78c49592f82b16221d32fa5160516` Hash scope: SHA-256 of 2c8_alphagenome_merged_splicing_scorer.py at the commit. The other two scripts at the same commit: 2c8_alphagenome_splicescorer.py 0c425043d31e02b1ca6fe0ce1120051352a0b2eae2571e70ce4f05f14114c151, 2c8_alphagenome_junctionscorer.py 9f260b27b06670505a903e8695ce020ac7432acd640a7041823d47c762bfbcec. Inspected artifact
Discrepancy id discrepancy-52a714eb6bb63442 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.discrepancy_id` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Discrepancy id discrepancy-52a714eb6bb63442 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 pages) Retrieved: 2026-11-01T14:45:27Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.discrepancy_id` Source artifact SHA-256: `07bd32fffc1b31c222d43b0b18c213928e3fe111cc71c02fe2f95e64e6f7a798` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. Inspected artifact
Discrepancy id discrepancy-52a714eb6bb63442 Context-only references	Alavi 2026 AlphaGenome scoring scripts at commit 2a3875de (marcel-2c8/splicing-model-eval-2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: marcel-2c8/splicing-model-eval-2026 commit 2a3875de6635d3c9b51c71c8018d23df0df98d37 (2026-10-31) Retrieved: 2026-11-01T14:48:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.discrepancy_id` Source artifact SHA-256: `84b4887ca3b44a6600d6a02046ab6de9d2f78c49592f82b16221d32fa5160516` Hash scope: SHA-256 of 2c8_alphagenome_merged_splicing_scorer.py at the commit. The other two scripts at the same commit: 2c8_alphagenome_splicescorer.py 0c425043d31e02b1ca6fe0ce1120051352a0b2eae2571e70ce4f05f14114c151, 2c8_alphagenome_junctionscorer.py 9f260b27b06670505a903e8695ce020ac7432acd640a7041823d47c762bfbcec. Inspected artifact
Claimed field discrepancy_review Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

3 source records and release history

Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Original source · bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 pages)
Alavi 2026 AlphaGenome scoring scripts at commit 2a3875de (marcel-2c8/splicing-model-eval-2026) · Original source · marcel-2c8/splicing-model-eval-2026 commit 2a3875de6635d3c9b51c71c8018d23df0df98d37 (2026-10-31)
Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages)

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Technical metadata and extraction receipts

Stable ID: discrepancy-review-20261101-alavi-alphagenome-splicing-rerun

areas: dna-genomes
contexts: clinical_research
field: discrepancy_review
discrepancy id: discrepancy-52a714eb6bb63442
previous ids: discrepancy-ead251c24ba272c1
revision: 3
value: confirmed-error
action: corrected-records
date: 2026-11-01
rationale: Version 2 of the preprint (posted 2026-10-31) prints AlphaGenome rows rerun with the 1-based position. It replaces version 1's three AlphaGenome rows with four: the composite score of AlphaGenome's splicing notebook, splice-site usage, splice-sites and splice-junctions. The splice-sites and splice-junctions rows rerun version 1's splice scorer and junction scorer scripts (the junction score now uses a natural-log fold change and both thresholds were re-tuned), so their 28 results replace the disputed version 1 results, which stay disputed and out of the release. The composite and splice-site usage rows are new configurations. Version 1's either-module row has no successor and stays disputed. The other models' cells are unchanged from version 1.
investigation url: https://github.com/rewire-bio/rewire-benchmark-data/issues/213
report url: https://github.com/marcel-2c8/splicing-model-eval-2026/issues/2
reported on: 2026-10-19
upstream response: The author committed the coordinate fix to both scripts on 2026-10-23 (da0cf43e, 4a5c9163), added a merged splicing scorer on 2026-10-30 (102a107f), posted the rerun as bioRxiv version 2 on 2026-10-31 and closed issue #2 the same day. The repository was renamed to splicing-model-eval-2026.
resolved by: rna-splicing-20261101-alavi2026-v2-source-article; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-composite-accuracy; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-composite-ppv; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-composite-sensitivity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-composite-specificity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-composite-type-i-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-composite-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-junctions-accuracy; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-junctions-ppv; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-junctions-sensitivity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-junctions-specificity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-junctions-type-i-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-junctions-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-site-usage-accuracy; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-site-usage-ppv; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-site-usage-sensitivity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-site-usage-specificity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-site-usage-type-i-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-site-usage-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-sites-accuracy; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-sites-ppv; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-sites-sensitivity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-sites-specificity; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-sites-type-i-error; rna-splicing-20261101-alavi2026-v2-result-multigene-alphagenome-splice-sites-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-composite-accuracy; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-composite-ppv; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-composite-sensitivity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-composite-specificity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-composite-type-i-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-composite-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-accuracy; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-ppv; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-sensitivity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-specificity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-type-i-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-site-usage-accuracy; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-site-usage-ppv; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-site-usage-sensitivity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-site-usage-specificity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-site-usage-type-i-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-site-usage-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-sites-accuracy; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-sites-ppv; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-sites-sensitivity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-sites-specificity; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-sites-type-i-error; rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-sites-type-ii-error; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-composite-positive-mutations; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-composite-positive-vus; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-splice-junctions-positive-mutations; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-splice-junctions-positive-vus; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-splice-site-usage-positive-mutations; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-splice-site-usage-positive-vus; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-splice-sites-positive-mutations; rna-splicing-20261101-alavi2026-v2-result-opa1-extended-positive-calls-alphagenome-splice-sites-positive-vus
source locator: rna-splicing-20261101-alavi2026-v2-source-article: Tables III and IV, AlphaGenome rows; Methods D. rna-splicing-20261101-alavi2026-v2-source-scoring-scripts: commit 2a3875de6635d3c9b51c71c8018d23df0df98d37, models/2_alphagenome. Upstream issue #2 state and closing date from the GitHub API.
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Claude agent for issue #213; no human review claimed. Extractor and reviewer were the same agent in the same session.; date: 2026-11-01; method note: Read version 2 Tables III and IV and Methods D, the scripts at the pinned commit, and the issue and commit history through the GitHub API.; note: Checked that resolved_by names the version 2 source and its 56 AlphaGenome results, and that each of the 28 rows of supersession.tsv pairs a version 2 result with the disputed version 1 result of the same protocol and column. Records a state change; nothing was reproduced. Verdict in docs/reviews/2026-11-01-alavi-v2-rerun.md.

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