Evidence claim

Relevance of HG003 ONT WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"

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

Use case: Select an execution workflow for large-scale diagnostic genomics
Assessed by: HG003 ONT WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Relevance: Proxy evidence
Endpoint: Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on ONT WGS at 10x to 50x

Gives accuracy for the same sample, platform and coverages as the runtime and memory table, so a reader can set accuracy beside resource use, which no previously linked source allows. Proxy: the tables do not say they come from the same runs, the DeepVariant version is unclear, and accuracy is measured against a single GIAB sample in its confident regions.

3 reviewed evaluations

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.

40 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
Citation locations 2 values source id model-execution-20261011-source-zheng2026-clair3-supplement locator Supplementary Table 3; Supplementary Notes source id model-execution-20261011-source-zheng2026-clair3 locator Results 3.1-3.2; Conflict of interests; Data availability Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.citation_locators` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id model-execution-20261011-source-zheng2026-clair3-supplement locator Supplementary Table 3; Supplementary Notes source id model-execution-20261011-source-zheng2026-clair3 locator Results 3.1-3.2; Conflict of interests; Data availability Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.citation_locators` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Comparison group zheng2026-hg003-accuracy Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.comparison_group` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group zheng2026-hg003-accuracy Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.comparison_group` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Comparison title Clair3 versus DeepVariant small-variant accuracy on HG003 (Zheng et al. 2026) Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.comparison_title` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Clair3 versus DeepVariant small-variant accuracy on HG003 (Zheng et al. 2026) Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.comparison_title` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources. Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.constraints` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources. Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.constraints` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Endpoint Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on ONT WGS at 10x to 50x Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.endpoint` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on ONT WGS at 10x to 50x Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability 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.endpoint` 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: use-case-mapping-model-execution-20261011-zheng2026-hg003-accuracy-ont

field: links:assessed_by:model-execution-20261011-protocol-zheng2026-hg003-accuracy-ont
value: model-execution-20261011-protocol-zheng2026-hg003-accuracy-ont
relevance: proxy
endpoint: Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on ONT WGS at 10x to 50x
rationale: Gives accuracy for the same sample, platform and coverages as the runtime and memory table, so a reader can set accuracy beside resource use, which no previously linked source allows. Proxy: the tables do not say they come from the same runs, the DeepVariant version is unclear, and accuracy is measured against a single GIAB sample in its confident regions.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources.
limitations: One value per configuration and coverage is printed; the number of runs behind it is not stated and no spread is printed.; Author-reported: the authors develop Clair3; DeepVariant was run by them.; Results 3.2 quote DeepVariant values at 10x and 20x ONT (SNP F1 94.68% and 98.79%) that differ from Supplementary Table 3 (94.89% and 99.17%); the text and the table may describe different DeepVariant versions.; No runtime is printed in this table.; The source has an unresolved evidence concern (Supplementary Tables 2 and 3 conflict with the Results text); see the source record.
revision: 1
reason: Add primary-source execution evidence from the diagnostic genomics execution literature pass (2026-10-11).
citation locators: source id: model-execution-20261011-source-zheng2026-clair3-supplement; locator: Supplementary Table 3; Supplementary Notes; source id: model-execution-20261011-source-zheng2026-clair3; locator: Results 3.1-3.2; Conflict of interests; Data availability
source locator: model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability
comparison group: zheng2026-hg003-accuracy
comparison title: Clair3 versus DeepVariant small-variant accuracy on HG003 (Zheng et al. 2026)
headline metric: f1-score
stratum label: ONT
stratum order: 1
review: method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent uc-execution extracted and drafted; Claude (Opus 5.5) review agent reviewer-exec checked every value and this judgement against the pinned sources; reviewed at: 2026-10-12T07:50:32Z; note: Bounded primary-source transcription with independent cell check and relevance review. No execution, reproduction, qualified human scientific review or clinical validation.
reviewed evaluations: model-execution-20261011-eval-zheng2026-clair3-accuracy-hg003-accuracy-ont; model-execution-20261011-eval-zheng2026-clair3-pileup-accuracy-hg003-accuracy-ont; model-execution-20261011-eval-zheng2026-deepvariant-accuracy-hg003-accuracy-ont
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