Long-read HiFi genome sequencing SNV/indel (<50 bp) accuracy
| 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 | 160,865 | 190,416 | 120,916 | 584,743 | 2,718,604 | 3,303,346 | 14,059 | 20,593 |
| Recall | 99.05% | 97.84% | 96.63% | 98.93% | 99.91% | 99.74% | 99.86% | 99.56% | |
| Precision | 99.54% | 99.81% | 99.67% | 99.80% | 99.99% | 99.95% | 99.98% | 99.96% | |
| Insertions (1–5 bp) | Count | 128,237 | 4241 | 4596 | 140,934 | 69,118 | 210,639 | 46 | 109 |
| Recall | 98.57% | 98.50% | 98.62% | 98.64% | 99.90% | 99.05% | 99.71% | 99.44% | |
| Precision | 98.42% | 99.14% | 98.98% | 98.53% | 99.94% | 98.99% | 100.00% | 99.35% | |
| Insertions (6–15 bp) | Count | 14,435 | 342 | 486 | 15,460 | 6496 | 22,004 | 5 | 42 |
| Recall | 98.67% | 98.39% | 98.77% | 98.70% | 99.73% | 99.00% | 100.00% | 99.58% | |
| Precision | 98.98% | 98.52% | 98.87% | 99.02% | 99.94% | 99.29% | 100.00% | 99.25% | |
| Insertions (≥16 bp) | Count | 2415 | 122 | 136 | 2747 | 2016 | 4776 | 2 | 13 |
| Recall | 98.76% | 96.91% | 97.86% | 98.80% | 99.80% | 99.22% | 85.71% | 97.52% | |
| Precision | 99.16% | 97.23% | 98.15% | 99.17% | 99.86% | 99.46% | 100.00% | 96.63% | |
| Deletions (1–5 bp) | Count | 136,024 | 4600 | 4507 | 148,953 | 69,677 | 218,129 | 59 | 142 |
| Recall | 98.78% | 98.45% | 98.26% | 98.82% | 99.87% | 99.15% | 99.48% | 99.00% | |
| Precision | 98.89% | 99.18% | 98.91% | 98.95% | 99.93% | 99.25% | 99.72% | 99.49% | |
| Deletions (6–15 bp) | Count | 16,664 | 466 | 544 | 17,758 | 6647 | 24,190 | 10 | 50 |
| Recall | 98.68% | 98.11% | 98.29% | 98.68% | 99.57% | 98.93% | 100.00% | 99.74% | |
| Precision | 98.88% | 98.64% | 98.40% | 98.90% | 99.86% | 99.15% | 100.00% | 99.74% | |
| Deletions (≥16 bp) | Count | 3424 | 152 | 116 | 3681 | 1621 | 5170 | 2 | 12 |
| Recall | 99.33% | 98.53% | 98.15% | 99.32% | 99.63% | 99.42% | 85.71% | 100.00% | |
| Precision | 99.49% | 98.93% | 98.15% | 99.49% | 99.88% | 99.61% | 100.00% | 100.00% | |
| All indels | Count | 285,386 | 9840 | 10,200 | 313,715 | 155,551 | 469,067 | 125 | 362 |
| Recall | 98.78% | 98.43% | 98.42% | 98.82% | 99.86% | 99.16% | 99.65% | 99.26% | |
| Precision | 98.70% | 99.09% | 98.89% | 98.78% | 99.93% | 99.14% | 99.88% | 99.38% | |
| SNVs and indels | Count | 462,064 | 200,340 | 131,301 | 914,275 | 2,874,179 | 3,788,255 | 14,184 | 20,961 |
| Recall | 98.81% | 97.87% | 96.78% | 98.85% | 99.91% | 99.65% | 99.86% | 99.55% | |
| Precision | 98.99% | 99.77% | 99.61% | 99.42% | 99.99% | 99.85% | 99.98% | 99.95% | |
[i] (indels) insertions/deletions, (RefSeq CDS) NCBI Reference Sequence gene coding sequence, (SNVs) single nucleotide variants.