Table 3.

Genotyping accuracy and rate of SVJedi-graph and state of the art genotyping tools on the deletions and insertions of the High confidence HG002 SV set, genotyped with PacBio CLR (30×), PacBio CCS (HiFi, 25×), and ONT (40×) reads.

	PacBio CLR		PacBio HiFi		ONT
Tool	Accuracy (%)	Rate (%)	Accuracy (%)	Rate (%)	Accuracy (%)	Rate (%)
SVJedi-graph	94.6	99.0	94.1	99.5	90.4	100.0
cuteSV	88.7	100.0	91.3	100.0	92.7	100.0
LRcaller	83.6	100.0	86.2	100.0	84.8	100.0
Sniffles2	85.4	99.5	89.4	99.2	88.9	99.8
SVJedi	92.2	90.2	81.3	84.4	90.7	86.2