Evidence claim

version: DeepVariant runs (Zheng et al. 2026)

Evidence concern: excluded from comparisons

Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2

Version of DeepVariant v1.10-beta GPU mode (Zheng et al. 2026)

Supplementary Table 2 and the Supplementary Notes command lines give DeepVariant v1.10-beta (google/deepvariant:v1.10-beta and v1.10-beta-gpu); Results 3.1 compare 'DeepVariant v1.8 in CPU and GPU modes'. Supplementary Table 3 prints no version.

Descriptive fact transcribed from the pinned source.

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.

12 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field version Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML Retrieved: 2026-10-11T21:42:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field version Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 Retrieved: 2026-10-11T21:42:40Z	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: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Source location Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML Retrieved: 2026-10-11T21:42:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 Retrieved: 2026-10-11T21:42:40Z	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.source_locator` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Claimed value Supplementary Table 2 and the Supplementary Notes command lines give DeepVariant v1.10-beta (google/deepvariant:v1.10-beta and v1.10-beta-gpu); Results 3.1 compare 'DeepVariant v1.8 in CPU and GPU modes'. Supplementary Table 3 prints no version. Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML Retrieved: 2026-10-11T21:42:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Supplementary Table 2 and the Supplementary Notes command lines give DeepVariant v1.10-beta (google/deepvariant:v1.10-beta and v1.10-beta-gpu); Results 3.1 compare 'DeepVariant v1.8 in CPU and GPU modes'. Supplementary Table 3 prints no version. Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 Retrieved: 2026-10-11T21:42:40Z	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.value` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Description Descriptive fact transcribed from the pinned source. Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML Retrieved: 2026-10-11T21:42:40Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Descriptive fact transcribed from the pinned source. Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 Retrieved: 2026-10-11T21:42:40Z	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: `description` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Relationship: subject model-execution-20261011-config-zheng2026-deepvariant-1-10-beta-gpu Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML Retrieved: 2026-10-11T21:42:40Z	not individually reviewed No individual claim review recorded Audit details Field: `links:subject:model-execution-20261011-config-zheng2026-deepvariant-1-10-beta-gpu` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: subject model-execution-20261011-config-zheng2026-deepvariant-1-10-beta-gpu Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 Retrieved: 2026-10-11T21:42:40Z	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: `links:subject:model-execution-20261011-config-zheng2026-deepvariant-1-10-beta-gpu` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Accelerated long-read variant calling with Clair3 for whole-genome sequencing · Original source · Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML
Accelerated long-read variant calling with Clair3: Supplementary Data · Original source · btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153

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Technical metadata and extraction receipts

Stable ID: model-execution-20261011-claim-zheng2026-deepvariant-version

field: version
value: Supplementary Table 2 and the Supplementary Notes command lines give DeepVariant v1.10-beta (google/deepvariant:v1.10-beta and v1.10-beta-gpu); Results 3.1 compare 'DeepVariant v1.8 in CPU and GPU modes'. Supplementary Table 3 prints no version.
source locator: Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1
review: method: source-hash-verification; pdf-text-parse; rendered-source-visual-check; independent-cell-check; method note: Re-downloaded the Europe PMC supplementaryFiles zip and matched the PDF member's SHA-256. Supplementary Table 1 parsed from pdftotext -layout with a separate review script; Supplementary Tables 2 and 3 read in full by the reviewer from the embedded image and a 250 dpi render of page 3, written down independently and compared cell by cell (350 cells). Article XML re-downloaded and matched.; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent reviewer-exec, independent of the extractor uc-execution; no human review claimed; reviewed at: 2026-10-12T07:50:32Z; artifact sha256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13141153/supplementaryFiles; note: Independent review 2026-10-12: printed value, numeric value, metric, qualifier, unit, direction, uncertainty, locator and configuration and protocol identity match the source. Transcribed, not reproduced.

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subject: DeepVariant v1.10-beta GPU mode (Zheng et al. 2026)

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