Table 4 Evaluation of insertions (\(\ge\)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
Insertions | flanking region (10kb) | flanking region (25kb) | flanking region (50kb) | flanking region (100kb) | |
|---|---|---|---|---|---|
50-1k | benchmark | 95 | |||
TP | 34 | 45 | 53 | 53 | |
TP_GT | 27 | 37 | 40 | 38 | |
FP | 6 | 12 | 18 | 22 | |
FN | 61 | 50 | 42 | 42 | |
Recall | 35.8% | 47.4% | 55.8% | 55.8% | |
Precision | 85.0% | 78.9% | 74.6% | 70.7% | |
F1 | 50.4% | 59.2% | 63.9% | 62.4% | |
GT_accuracy | 79.4% | 82.2% | 75.5% | 71.7% | |
1k-10k | benchmark | 16 | |||
TP | 1 | 1 | 1 | 1 | |
TP_GT | 0 | 0 | 0 | 0 | |
FP | 0 | 0 | 0 | 0 | |
FN | 15 | 15 | 15 | 15 | |
Recall | 6.2% | 6.2% | 6.2% | 6.2% | |
Precision | 100.0% | 100.0% | 100.0% | 100.0% | |
F1 | 11.8% | 11.8% | 11.8% | 11.8% | |
GT_accuracy | 0.0% | 0.0% | 0.0% | 0.0% | |