Dataset

GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x

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

HG003 reads subsampled with samtools view -s to stated coverages; GIAB v4.2.1 truth on GRCh38.

Evaluation results

6 evaluations · 187 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	88 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 10x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	6,781 Mean memory (Variant calling from BAM, whole run; HG003 PacBio 10x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	41,832 Peak memory (Variant calling from BAM, whole run; HG003 PacBio 10x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	14 Runtime (Variant calling from BAM, whole run; HG003 PacBio 10x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 10x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	98 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 20x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	5,758 Mean memory (Variant calling from BAM, whole run; HG003 PacBio 20x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	52,578 Peak memory (Variant calling from BAM, whole run; HG003 PacBio 20x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	13 Runtime (Variant calling from BAM, whole run; HG003 PacBio 20x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 20x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	128 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 30x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	8,034 Mean memory (Variant calling from BAM, whole run; HG003 PacBio 30x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	49,319 Peak memory (Variant calling from BAM, whole run; HG003 PacBio 30x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	12 Runtime (Variant calling from BAM, whole run; HG003 PacBio 30x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 30x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	125 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 40x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	7,985 Mean memory (Variant calling from BAM, whole run; HG003 PacBio 40x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	46,024 Peak memory (Variant calling from BAM, whole run; HG003 PacBio 40x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	12 Runtime (Variant calling from BAM, whole run; HG003 PacBio 40x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 40x, column 'Runtime (minutes)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	139 Data io volume (Variant calling from BAM, whole run; HG003 PacBio 50x) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Total data movement IO (GB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	5,489 Mean memory (Variant calling from BAM, whole run; HG003 PacBio 50x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Average memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	55,095 Peak memory (Variant calling from BAM, whole run; HG003 PacBio 50x) megabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Peak memory (MB)'
Configuration: Clair3 v1.2.0 GPU mode (Zheng et al. 2026)	Protocol: HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) Dataset: GIAB HG003 whole genome, PacBio Revio (2022Q4 release), subsampled to 10x-50x	12 Runtime (Variant calling from BAM, whole run; HG003 PacBio 50x) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked 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, coverage and source Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026) model-execution-20261011-protocol-zheng2026-hg003-resource-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 2 (image, page 2), sample 'HG003 WGS', platform 'PacBio Revio', caller 'Clair3 v1.2.0 (GPU mode)', read coverage 50x, column 'Runtime (minutes)'
Configuration: Clair3, 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	91.4% 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	Author-reported evaluation · Source checked 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, coverage and source Clair3, 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 'Clair3', column 'Indel F1-score'
Configuration: Clair3, 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	94.2% 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	Author-reported evaluation · Source checked 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, coverage and source Clair3, 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 'Clair3', column 'Indel Precision'
Configuration: Clair3, 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	88.7% 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	Author-reported evaluation · Source checked 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, coverage and source Clair3, 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 'Clair3', column 'Indel Recall'
Configuration: Clair3, 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	97.6% 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	Author-reported evaluation · Source checked 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, coverage and source Clair3, 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 'Clair3', column 'Overall F1-score'
Configuration: Clair3, 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	98.6% 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	Author-reported evaluation · Source checked 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, coverage and source Clair3, 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 'Clair3', column 'Overall Precision'

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

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

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Inspect claims, sources and review details

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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
Accession PacBio Revio HG002-HG004 GRCh38 (https://downloads.pacbcloud.com/public/revio/2022Q4/) Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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.accession` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Accession PacBio Revio HG002-HG004 GRCh38 (https://downloads.pacbcloud.com/public/revio/2022Q4/) Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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.accession` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Population One GIAB sample (HG003, NA24149) at 10x, 20x, 30x, 40x and 50x coverage Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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.population` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One GIAB sample (HG003, NA24149) at 10x, 20x, 30x, 40x and 50x coverage Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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.population` 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 Notes 'Data availability' and 'BAM subsampling'; Results 3.2 Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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 Notes 'Data availability' and 'BAM subsampling'; Results 3.2 Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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
Split HG003 is held out from Clair3 and DeepVariant training (Results 3.2) Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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.split` Source artifact SHA-256: `99ef4db5251a77e6fb9137aa3699b4dac93bdef2aff99de91c4d24ca5fc6a965` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split HG003 is held out from Clair3 and DeepVariant training (Results 3.2) Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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.split` Source artifact SHA-256: `feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9` Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf Inspected artifact
Description HG003 reads subsampled with samtools view -s to stated coverages; GIAB v4.2.1 truth on GRCh38. Context-only references	Accelerated long-read variant calling with Clair3 for whole-genome sequencing Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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 HG003 reads subsampled with samtools view -s to stated coverages; GIAB v4.2.1 truth on GRCh38. Context-only references	Accelerated long-read variant calling with Clair3: Supplementary Data Original source ↗ Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2 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

How to read the evidence

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-data-zheng2026-hg003-pacbio-revio

areas: dna-genomes
contexts: research
accession: PacBio Revio HG002-HG004 GRCh38 (https://downloads.pacbcloud.com/public/revio/2022Q4/)
population: One GIAB sample (HG003, NA24149) at 10x, 20x, 30x, 40x and 50x coverage
split: HG003 is held out from Clair3 and DeepVariant training (Results 3.2)
source locator: Supplementary Notes 'Data availability' and 'BAM subsampling'; Results 3.2
missing metadata: version: reason: unreported; note: Release folder named; no file checksums given

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