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.

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