Table 3 Evaluation of deletions (\(\ge\)50bp) on chromosome 21 in HG002 from 10x linked-reads by different lengths of flanking regions in RegionIndel
From: Large indel detection in region-based phased diploid assemblies from linked-reads
Deletions | flanking region (10kb) | flanking region (25kb) | flanking region (50kb) | flanking region (100kb) | |
|---|---|---|---|---|---|
50-1k | benchmark | 58 | |||
TP | 50 | 55 | 55 | 56 | |
TP_GT | 45 | 48 | 52 | 51 | |
FP | 40 | 59 | 88 | 117 | |
FN | 8 | 3 | 3 | 2 | |
Recall | 86.2% | 94.8% | 94.8% | 96.6% | |
Precision | 55.6% | 48.2% | 38.5% | 32.4% | |
F1 | 67.6% | 64.0% | 54.7% | 48.5% | |
GT_accuracy | 90.0% | 87.3% | 94.6% | 91.1% | |
1k-10k | benchmark | 7 | |||
TP | 7 | 7 | 7 | 7 | |
TP_GT | 7 | 7 | 7 | 7 | |
FP | 0 | 1 | 1 | 1 | |
FN | 0 | 0 | 0 | 0 | |
Recall | 100.0% | 100.0% | 100.0% | 100.0% | |
Precision | 100.0% | 87.5% | 87.5% | 87.5% | |
F1 | 100.0% | 93.3% | 93.3% | 93.3% | |
GT_accuracy | 100.0% | 100.0% | 100.0% | 100.0% | |