Table 1 Evaluation of deletions (\(\ge\)50bp) in HG002 by RegionIndel, Aquila, Aquila_stLFR, LinkedSV, and Novel-X (chrX and chrY were excluded in the evaluation). Abbreviations: true positives (TP), false positives (FP), false negatives (FN), and genotype (GT)
From: Large indel detection in region-based phased diploid assemblies from linked-reads
Deletions | stLFR | 10x | |||||||
|---|---|---|---|---|---|---|---|---|---|
RegionIndel | Aquila_stLFR | LinkedSV | Novel-X | RegionIndel | Aquila | LinkedSV | Novel-X | ||
50-1k | benchmark | 3605 | |||||||
TP | 2563 | 2963 | 8 | NaN | 3210 | 3318 | 2013 | NaN | |
TP_GT | 2116 | 2547 | NaN | NaN | 2796 | 3001 | NaN | NaN | |
FP | 1773 | 8484 | 0 | NaN | 1927 | 6439 | 215 | NaN | |
FN | 1042 | 642 | 3597 | NaN | 395 | 287 | 1592 | NaN | |
Recall | 71.1% | 82.2% | 0.2% | NaN | 89.0% | 92.0% | 55.8% | NaN | |
Precision | 59.1% | 25.9% | 100.0% | NaN | 62.5% | 34.0% | 90.4% | NaN | |
F1 | 64.6% | 39.4% | 0.4% | NaN | 73.4% | 49.7% | 69.0% | NaN | |
GT_accuracy | 82.6% | 86.0% | NaN | NaN | 87.1% | 90.4% | NaN | NaN | |
1k-10k | benchmark | 481 | |||||||
TP | 296 | 317 | 92 | NaN | 419 | 365 | 361 | NaN | |
TP_GT | 252 | 293 | NaN | NaN | 390 | 339 | NaN | NaN | |
FP | 133 | 285 | 20 | NaN | 51 | 90 | 54 | NaN | |
FN | 185 | 164 | 389 | NaN | 62 | 116 | 120 | NaN | |
Recall | 61.5% | 65.9% | 19.1% | NaN | 87.1% | 75.9% | 75.1% | NaN | |
Precision | 69.0% | 52.7% | 82.1% | NaN | 89.1% | 80.2% | 87.0% | NaN | |
F1 | 65.1% | 58.5% | 31.0% | NaN | 88.1% | 78.0% | 80.6% | NaN | |
GT_accuracy | 85.1% | 92.4% | NaN | NaN | 93.1% | 92.9% | NaN | NaN | |
>10k | benchmark | 29 | |||||||
TP | 8 | 6 | 27 | NaN | 16 | 7 | 29 | NaN | |
TP_GT | 8 | 6 | NaN | NaN | 16 | 7 | NaN | NaN | |
FP | 45 | 99 | 3 | NaN | 16 | 49 | 25 | NaN | |
FN | 21 | 23 | 2 | NaN | 13 | 22 | 0 | NaN | |
Recall | 27.6% | 20.7% | 93.1% | NaN | 55.2% | 24.1% | 100.0% | NaN | |
Precision | 15.1% | 5.7% | 90.0% | NaN | 50.0% | 12.5% | 53.7% | NaN | |
F1 | 19.5% | 9.0% | 91.5% | NaN | 52.5% | 16.5% | 69.9% | NaN | |
GT_accuracy | 100.0% | 100.0% | NaN | NaN | 100.0% | 100.0% | NaN | NaN | |
\(\ge\)50bp (overall) | benchmark | 4116 | |||||||
TP | 2871 | 3286 | 142 | NaN | 3648 | 3694 | 2408 | NaN | |
TP_GT | 2380 | 2846 | NaN | NaN | 3204 | 3350 | NaN | NaN | |
FP | 1947 | 8868 | 8 | NaN | 1990 | 6571 | 289 | NaN | |
FN | 1245 | 830 | 3974 | NaN | 468 | 422 | 1708 | NaN | |
Recall | 69.8% | 79.8% | 3.4% | NaN | 88.6% | 89.7% | 58.5% | NaN | |
Precision | 59.6% | 27.0% | 94.7% | NaN | 64.7% | 36.0% | 89.3% | NaN | |
F1 | 64.3% | 40.4% | 6.7% | NaN | 74.8% | 51.4% | 70.7% | NaN | |
GT_accuracy | 82.9% | 86.6% | NaN | NaN | 87.8% | 90.7% | NaN | NaN | |