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Evaluation

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

Published execution benchmark; transcribed, not reproduced.

Evaluation results

1 evaluation · 45 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		91.1% F1 (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'Indel F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		93.2% Precision (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'Indel Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		89.1% Recall (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'Indel Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		96.9% F1 (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'Overall F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		98.5% Precision (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'Overall Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		95.4% Recall (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'Overall Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		97.8% F1 (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'SNP F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.3% Precision (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'SNP Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		96.4% Recall (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 10x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 10x, caller 'DeepVariant', column 'SNP Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		97.8% F1 (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'Indel F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		97.8% Precision (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'Indel Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		97.7% Recall (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'Indel Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.5% F1 (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'Overall F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.6% Precision (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'Overall Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.5% Recall (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'Overall Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.8% F1 (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'SNP F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.8% Precision (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'SNP Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.7% Recall (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 20x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 20x, caller 'DeepVariant', column 'SNP Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99% F1 (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'Indel F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99% Precision (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'Indel Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99% Recall (Indel; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'Indel Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.8% F1 (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'Overall F1-score'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.8% Precision (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'Overall Precision'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.8% Recall (SNPs and indels; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'Overall Recall'
Configuration: DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)Protocol: HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x		99.9% F1 (SNP; GIAB v4.2.1 HG003 confident regions; PacBio 30x)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)

model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio

Aggregation: Not reported

Accelerated 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 'PacBio Revio', read coverage 30x, caller 'DeepVariant', column 'SNP F1-score'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)

Configuration
DeepVariant, accuracy runs (Zheng et al. 2026 Supplementary Table 3)
Protocol
HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
Dataset
GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x
origin
Independent external evaluation
configuration
Primary source as retrieved 2026-10-11
protocol id
model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio
dataset version
Not reported
split
HG003 subsampled to 10x, 20x, 30x, 40x and 50x
population
One GIAB sample (HG003)
inputs
Aligned reads (BAM) and GRCh38 reference
adaptation
Not reported
metric implementation
hap.py 0.3.12, vcfeval engine, PASS only
aggregation
One value per coverage and variant class
budget
One value per caller and coverage; number of runs and hardware not stated in the table

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

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.

36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Comparison: adaptation
Not reported
Context-only references		Accelerated long-read variant calling with Clair3 for whole-genome sequencing

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: adaptation
Not reported
Context-only references		Accelerated long-read variant calling with Clair3: Supplementary Data

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

missing or unspecified

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9

Hash scope: Hash scope not separately documented; inspect source record

Archive member: btag181_supplementary_data.pdf

Inspected artifact

Comparison: aggregation
One value per coverage and variant class
Context-only references		Accelerated long-read variant calling with Clair3 for whole-genome sequencing

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

independent paper

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: aggregation
One value per coverage and variant class
Context-only references		Accelerated long-read variant calling with Clair3: Supplementary Data

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9

Hash scope: Hash scope not separately documented; inspect source record

Archive member: btag181_supplementary_data.pdf

Inspected artifact

Comparison: budget
One value per caller and coverage; number of runs and hardware not stated in the table
Context-only references		Accelerated long-read variant calling with Clair3 for whole-genome sequencing

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

independent paper

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: budget
One value per caller and coverage; number of runs and hardware not stated in the table
Context-only references		Accelerated long-read variant calling with Clair3: Supplementary Data

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9

Hash scope: Hash scope not separately documented; inspect source record

Archive member: btag181_supplementary_data.pdf

Inspected artifact

Comparison: dataset version
Not reported
Context-only references		Accelerated long-read variant calling with Clair3 for whole-genome sequencing

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: dataset version
Not reported
Context-only references		Accelerated long-read variant calling with Clair3: Supplementary Data

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

missing or unspecified

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9

Hash scope: Hash scope not separately documented; inspect source record

Archive member: btag181_supplementary_data.pdf

Inspected artifact

Comparison: inputs
Aligned reads (BAM) and GRCh38 reference
Context-only references		Accelerated long-read variant calling with Clair3 for whole-genome sequencing

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

independent paper

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: inputs
Aligned reads (BAM) and GRCh38 reference
Context-only references		Accelerated long-read variant calling with Clair3: Supplementary Data

Original source ↗

Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'

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

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9

Hash scope: Hash scope not separately documented; inspect source record

Archive member: btag181_supplementary_data.pdf

Inspected artifact

How to read the evidence

Sources and history

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

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: model-execution-20261011-eval-zheng2026-deepvariant-accuracy-hg003-accuracy-pacbio

areas
dna-genomes
contexts
research
origin
independent_paper
protocol
model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio
version
Primary source as retrieved 2026-10-11
comparison
protocol id: model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio; dataset version: Not reported; split: HG003 subsampled to 10x, 20x, 30x, 40x and 50x; population: One GIAB sample (HG003); inputs: Aligned reads (BAM) and GRCh38 reference; adaptation: Not reported; metric implementation: hap.py 0.3.12, vcfeval engine, PASS only; aggregation: One value per coverage and variant class; budget: One value per caller and coverage; number of runs and hardware not stated in the table
source locator
Supplementary Table 3, platform 'PacBio Revio', caller 'DeepVariant'
missing metadata
comparison.dataset version: reason: unreported
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