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. 2023 Jan 17;14:283. doi: 10.1038/s41467-023-35996-1

Table 1.

SV discovery accuracy on simulated datasets

DeBreak Sniffles pbsv cuteSV
Type Rec Pre F1 Rec Pre F1 Rec Pre F1 Rec Pre F1
PacBio
DEL 99.59 99.50 99.54 95.50 99.83 97.62 97.21 99.58 98.38 96.94 99.82 98.36
INS 98.51 99.65 99.08 92.35 99.52 95.80 95.38 96.22 95.80 94.58 94.71 94.64
DUP 98.27 97.04 97.65 90.80 98.63 94.55 44.53 97.11 60.97 44.13 99.03 61.05
INV 99.10 99.40 99.25 94.57 97.22 95.88 82.67 99.92 90.47 96.53 50.00 65.88
TRA 99.17 99.67 99.41 97.67 95.60 96.62 97.67 25.04 39.86 99.00 50.30 66.70
Total 99.02 99.45 99.23 93.85 99.47 96.58 93.36 95.34 94.34 93.50 92.39 92.94
Nanopore
DEL 98.08 98.82 98.45 94.83 98.72 96.74 98.65 98.55 98.60 97.87 98.27 98.07
INS 98.17 99.68 98.92 92.70 99.73 96.09 97.05 95.92 96.48 96.04 94.01 95.01
DUP 97.00 93.60 95.27 91.97 98.37 95.06 46.03 87.37 60.23 39.67 99.50 56.72
INV 91.63 98.71 95.04 93.67 95.18 94.41 88.20 99.96 93.71 97.37 50.00 66.07
TRA 92.83 99.83 96.17 97.17 91.38 94.18 97.83 25.26 40.15 99.17 50.17 66.63
Total 97.73 98.96 98.35 93.71 98.91 96.24 95.08 94.60 94.84 94.41 91.46 92.91

The unit for recall, precision, and F1 score is %. The highest recall, precision, and F1 score among four tested SV callers are marked in bold.

Rec Recall, Pre Precision, F1 F1 score.