BMC Genomic Data

Table 3 Model fitness measured by Akaike information criterion (AIC) in scenario 3

From: Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle

		All MAF^a		High MAF^a		Low MAF^a
SNP^b	Prediction model^c	Mean	SD	Mean	SD	Mean	SD
7 K	Model (1) with G_V	6164	63	6145	66	6191	61
	Model (1) with G_Y	6162	63	6145	66	6188	61
	Model (1) with G_S	6162	63	6146	66	6187	61
	Model (2)	6163	63	6147	66	6186	61
50 K	Model (1) with G_V	6159	63	6139	65	6188	62
	Model (1) with G_Y	6155	63	6139	65	6181	62
	Model (1) with G_S	6155	63	6142	65	6175	62
	Model (2)	6155	63	6140	65	6163	62
7K_to_HD	Model (1) with G_V	6158	63	6138	65	6189	62
	Model (1) with G_Y	6155	63	6138	65	6182	62
	Model (1) with G_S	6156	63	6147	65	6171	62
	Model (2)	6154	63	6139	65	6155	62
50K_to_HD	Model (1) with G_V	6157	63	6137	65	6188	62
	Model (1) with G_Y	6154	63	6137	65	6181	62
	Model (1) with G_S	6155	63	6146	65	6169	62
	Model (2)	6153	63	6138	65	6152	62
HD	Model (1) with G_V	6157	63	6136	65	6188	62
	Model (1) with G_Y	6154	63	6137	65	6180	62
	Model (1) with G_S	6155	63	6147	65	6168	62
	Model (2)	6152	63	6138	65	6150	62

^aMAF, Minor allele frequency; All MAF, 0.01 ≤ MAF ≤ 0.5; High MAF, 0.05 < MAF ≤ 0.5; Low MAF, 0.01 ≤ MAF ≤ 0.05
^b7K, 50 K and HD, Illumina infinium BovineLDv1.1, BovineSNP50v2, and BovineHD BeadChips, respectively; 7 K_to_HD and 50 K_to_HD, Imputations were performed from 7 K and 50 K to HD, respectively
^cG_V, VanRaden's genome relationship matrix (GRM); G_Y, Yang's GRM; G_S, Speed's GRM

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