X-CNV: genome-wide prediction of the pathogenicity of copy number variations

Table 1 Model performance of X-CNV, AnnotSV, and ClassifyCNV on the independent validation set

Metrics	X-CNV			AnnotSV			ClassifyCNV
	All	Gain	Loss	All	Gain	Loss	All	Gain	Loss
MCC	0.65	0.41	0.70	0.27	0.06	0.46	− 0.08	− 0.24	0.01
Accuracy	0.83	0.75	0.88	0.62	0.38	0.79	0.48	0.34	0.57
F1 score	0.84	0.58	0.92	0.73	0.49	0.88	0.56	0.32	0.68
Fowlkes–Mallows index	0.84	0.58	0.92	0.76	0.56	0.87	0.56	0.34	0.68
Sensitivity	0.85	0.52	0.96	0.96	0.92	0.98	0.62	0.47	0.68
Specificity	0.8	0.86	0.70	0.21	0.13	0.35	0.31	0.28	0.34

ISSN: 1756-994X