Result

F1 (Indel; GIAB v4.2.1 HG003 confident regions; ONT 10x) of Clair3 pileup-only calls (Zheng et al. 2026 Supplementary Table 3) on GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x

64.5% F1 (Indel; GIAB v4.2.1 HG003 confident regions; ONT 10x)

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

Methods

Tested configuration: Clair3 pileup-only calls (Zheng et al. 2026 Supplementary Table 3)
Protocol: HG003 ONT WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, ONT R10.4.1 5 kHz (EPI2ME giab-2025.01), subsampled to 10x-50x
Procedure: HG003 ONT WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Evaluation: Clair3 pileup, HG003 ONT small-variant accuracy (Zheng et al. 2026)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Author-reported evaluation · source checkedAccelerated long-read variant calling with Clair3 for whole-genome sequencing; Accelerated long-read variant calling with Clair3: Supplementary Data · Supplementary Table 3 (image, page 3), platform 'ONT r10.4.1 5kHz', read coverage 10x, caller 'Clair3 pileup', column 'Indel F1-score'

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: HG003 subsampled to 10x, 20x, 30x, 40x and 50x
Adaptation: Not reported
Scoring implementation: hap.py 0.3.12, vcfeval engine, PASS only

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.

2 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
Reported result 64.49% Individual claims	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Table 3 (image, page 3), platform 'ONT r10.4.1 5kHz', read coverage 10x, caller 'Clair3 pileup', column 'Indel F1-score' 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	source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-12T07:50:32Z author reported Audit details 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. Field: `attributes.printed_value` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Extraction artifact
Reported result 64.49% Individual claims	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Table 3 (image, page 3), platform 'ONT r10.4.1 5kHz', read coverage 10x, caller 'Clair3 pileup', column 'Indel F1-score' 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	source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-12T07:50:32Z author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details 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. Field: `attributes.printed_value` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact Extraction artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Extraction 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-result-zheng2026-clair3-pileup-accuracy-hg003-accuracy-ont-10x-indel-f1-score

metric: f1-score
metric direction: higher
unit: percent
metric qualifier: Indel; GIAB v4.2.1 HG003 confident regions; ONT 10x
printed value: 64.49%
numeric value: 64.49
source locator: Supplementary Table 3 (image, page 3), platform 'ONT r10.4.1 5kHz', read coverage 10x, caller 'Clair3 pileup', column 'Indel F1-score'
missing metadata: uncertainty: reason: unreported
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.

Related records

evaluation: Clair3 pileup, HG003 ONT small-variant accuracy (Zheng et al. 2026)

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