Table 4.

Correlation rates of the GWAS-top 0.5%, 1%, 2%, and 3% marker-sets and whole marker-set.

Data	Phenotype	Selected markersa	RRB (train/val./test)	RF (train/val./test)	DNN (train/val./test)	CNN (train/val./test)
Rice	DTF	184	0.838/0.777/0.343	0.935/0.641/0.330	0.914/0.727/0.328	0.862/0.686/0.301
		369	0.890/0.709/0.480	0.963/0.570/0.464	0.945/0.717/0.412	0.905/0.656/0.410
		738	0.919/0.715/0.478	0.968/0.621/0.484	0.962/0.726/0.406	0.925/0.734/0.468
		1107	0.940/0.715/0.448	0.968/0.644/0.485	0.966/0.713/0.486	0.931/0.659/0.439
		All	0.844/0.412/0.515	0.964/0.398/0.529	0.899/0.366/0.512	0.923/0.363/0.504
	PC	184	0.816/0.744/0.366	0.947/0.500/0.376	0.851/0.664/0.304	0.834/0.680/0.308
		369	0.871/0.717/0.517	0.960/0.524/0.471	0.844/0.624/0.486	0.872/0.555/0.387
		738	0.917/0.761/0.508	0.963/0.513/0.521	0.874/0.619/0.532	0.891/0.708/0.402
		1107	0.944/0.760/0.545	0.968/0.495/0.537	0.958/0.776/0.531	0.912/0.732/0.422
		All	0.874/0.449/0.473	0.968/0.326/0.542	0.902/0.554/0.521	0.917/0.415/0.400
	PH	184	0.914/0.834/0.494	0.971/0.787/0.578	0.931/0.795/0.492	0.944/0.814/0.586
		369	0.946/0.859/0.571	0.976/0.808/0.617	0.934/0.823/0.579	0.950/0.772/0.643
		738	0.970/0.869/0.566	0.980/0.830/0.646	0.956/0.875/0.527	0.952/0.865/0.527
		1107	0.982/0.897/0.636	0.979/0.849/0.661	0.964/0.890/0.603	0.955/0.879/0.669
		All	0.985/0.733/0.631	0.972/0.737/0.548	0.912/0.765/0.624	0.972/0.737/0.548
SOY	DTF	478	0.641/0.558/0.578	0.744/0.644/0.627	0.663/0.660/0.628	0.566/0.578/0.584
		957	0.832/0.795/0.705	0.957/0.778/0.725	0.825/0.763/0.705	0.634/0.636/0.656
		1914	0.905/0.840/0.757	0.974/0.775/0.764	0.897/0.825/0.747	0.846/0.804/0.739
		2871	0.944/0.872/0.767	0.978/0.809/0.771	0.938/0.850/0.746	0.810/0.804/0.753
		All	0.973/0.743/0.753	0.976/0.752/0.760	0.921/0.751/0.763	0.904/0.721/0.748

Highest correlation rates in each phenotype are shown in bold.

^aRows of each phenotype represent the number of GWAS top 0.5%, 1%, 2%, and 3%, and all markers in order.