Table 2 Evaluation of insertions (\(\ge\)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
Insertions | stLFR | 10x | |||||||
|---|---|---|---|---|---|---|---|---|---|
RegionIndel | Aquila_stLFR | LinkedSV | Novel-X | RegionIndel | Aquila | LinkedSV | Novel-X | ||
50-1k | benchmark | 4561 | |||||||
TP | 1199 | 1158 | NaN | 182 | 2522 | 2335 | NaN | 273 | |
TP_GT | 913 | 823 | NaN | NaN | 1964 | 1653 | NaN | NaN | |
FP | 80 | 211 | NaN | 19 | 434 | 2837 | NaN | 1003 | |
FN | 3362 | 3403 | NaN | 4379 | 2039 | 2226 | NaN | 4288 | |
Recall | 26.3% | 25.4% | NaN | 4.0% | 55.3% | 51.2% | NaN | 6.0% | |
Precision | 93.7% | 84.6% | NaN | 90.5% | 85.3% | 45.1% | NaN | 21.4% | |
F1 | 41.1% | 39.1% | NaN | 7.6% | 67.1% | 48.0% | NaN | 9.4% | |
GT_accuracy | 76.1% | 71.1% | NaN | NaN | 77.9% | 70.8% | NaN | NaN | |
1k-10k | benchmark | 696 | |||||||
TP | 5 | 2 | NaN | 15 | 32 | 17 | NaN | 46 | |
TP_GT | 1 | 1 | NaN | NaN | 14 | 1 | NaN | NaN | |
FP | 6 | 4 | NaN | 1 | 6 | 6 | NaN | 11 | |
FN | 691 | 694 | NaN | 681 | 664 | 679 | NaN | 650 | |
Recall | 0.7% | 0.3% | NaN | 2.2% | 4.6% | 2.4% | NaN | 6.6% | |
Precision | 45.5% | 33.3% | NaN | 93.8% | 84.2% | 73.9% | NaN | 80.7% | |
F1 | 1.4% | 0.6% | NaN | 4.2% | 8.7% | 4.7% | NaN | 12.2% | |
GT_accuracy | 20.0% | 50.0% | NaN | NaN | 43.8% | 5.9% | NaN | NaN | |
\(\ge\)50bp (overall) | benchmark | 5281 | |||||||
TP | 1204 | 1160 | NaN | 197 | 2554 | 2354 | NaN | 322 | |
TP_GT | 914 | 824 | NaN | NaN | 1978 | 1654 | NaN | NaN | |
FP | 81 | 215 | NaN | 16 | 434 | 2835 | NaN | 991 | |
FN | 4077 | 4121 | NaN | 5084 | 2727 | 2927 | NaN | 4959 | |
Recall | 22.8% | 22.0% | NaN | 3.7% | 48.4% | 44.6% | NaN | 6.1% | |
Precision | 93.7% | 84.4% | NaN | 92.5% | 85.5% | 45.4% | NaN | 24.5% | |
F1 | 36.7% | 34.9% | NaN | 7.2% | 61.8% | 45.0% | NaN | 9.8% | |
GT_accuracy | 75.9% | 71.0% | NaN | NaN | 77.4% | 70.3% | NaN | NaN | |