Table 2.
Long-read HiFi genome sequencing SNV/indel (<50 bp) reproducibility (GIAB high confidence)
| Genome-wide | RefSeq CDS | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Low complexity | Low mappability | Segmental duplications | All difficult regions | Not in any difficult region | All | Not in any difficult region | All | ||
| SNVs | Count | 170,332 | 181,786 | 113,753 | 584,487 | 2,721,331 | 3,305,818 | 14,023 | 20,467 |
| Concordance | 99.10% | 99.51% | 99.30% | 99.54% | 99.95% | 99.88% | 99.91% | 99.85% | |
| Insertions (1–5 bp) | Count | 139,069 | 4085 | 4495 | 151,456 | 69,083 | 221,146 | 48 | 115 |
| Concordance | 97.41% | 99.38% | 99.26% | 97.61% | 99.94% | 98.35% | 99.66% | 99.17% | |
| Insertions (6–15 bp) | Count | 15,335 | 335 | 490 | 16,341 | 6487 | 22,882 | 5 | 43 |
| Concordance | 98.13% | 98.99% | 99.31% | 98.23% | 99.96% | 98.74% | 100.00% | 100.00% | |
| Insertions (≥16 bp) | Count | 2527 | 118 | 119 | 2805 | 1847 | 4664 | 2 | 12 |
| Concordance | 98.22% | 97.70% | 98.01% | 98.31% | 99.84% | 98.93% | 100.00% | 95.22% | |
| Deletions (1–5 bp) | Count | 150,504 | 4459 | 4313 | 163,229 | 69,693 | 232,407 | 58 | 141 |
| Concordance | 98.13% | 99.35% | 99.21% | 98.25% | 99.97% | 98.77% | 99.72% | 99.41% | |
| Deletions (6–15 bp) | Count | 17,426 | 457 | 552 | 18,499 | 6652 | 24,940 | 10 | 47 |
| Concordance | 98.38% | 99.17% | 98.96% | 98.46% | 99.96% | 98.86% | 100.00% | 100.00% | |
| Deletions (≥16 bp) | Count | 3525 | 160 | 101 | 3771 | 1583 | 5220 | 3 | 16 |
| Concordance | 99.21% | 98.92% | 99.01% | 99.26% | 99.96% | 99.50% | 100.00% | 100.00% | |
| All indels | Count | 311,652 | 9518 | 9877 | 339,360 | 155,318 | 494,492 | 125 | 370 |
| Concordance | 97.90% | 99.32% | 99.21% | 98.05% | 99.95% | 98.64% | 99.73% | 99.37% | |
| SNVs and indels | Count | 498,720 | 191,398 | 123,824 | 940,587 | 2,876,675 | 3,817,077 | 14,148 | 20,841 |
| Concordance | 98.27% | 99.50% | 99.30% | 98.96% | 99.95% | 99.71% | 99.91% | 99.84% | |
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(indels) insertions/deletions, (RefSeq CDS) NCBI Reference Sequence gene coding sequence, (SNVs) single nucleotide variants.
