BMC Genomic Data

Table 2 Heritability estimation 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	0.28	0.05	0.32	0.05	0.20	0.06
	Model (1) with G_Y	0.30	0.05	0.33	0.05	0.23	0.06
	Model (1) with G_S	0.30	0.05	0.33	0.05	0.24	0.06
	Model (2)	0.30	0.05	0.33	0.05	0.23	0.06
50 K	Model (1) with G_V	0.33	0.06	0.38	0.06	0.24	0.06
	Model (1) with G_Y	0.36	0.06	0.39	0.06	0.30	0.06
	Model (1) with G_S	0.38	0.06	0.40	0.06	0.34	0.07
	Model (2)	0.37	0.06	0.39	0.06	0.34	0.06
7K_to_HD	Model (1) with G_V	0.34	0.06	0.39	0.06	0.24	0.06
	Model (1) with G_Y	0.37	0.06	0.40	0.06	0.30	0.06
	Model (1) with G_S	0.41	0.07	0.41	0.07	0.39	0.07
	Model (2)	0.39	0.06	0.40	0.06	0.38	0.06
50K_to_HD	Model (1) with G_V	0.34	0.06	0.39	0.06	0.25	0.06
	Model (1) with G_Y	0.37	0.06	0.41	0.06	0.30	0.07
	Model (1) with G_S	0.41	0.07	0.42	0.07	0.40	0.07
	Model (2)	0.40	0.06	0.40	0.06	0.40	0.06
HD	Model (1) with G_V	0.35	0.06	0.39	0.06	0.25	0.06
	Model (1) with G_Y	0.38	0.06	0.41	0.06	0.31	0.07
	Model (1) with G_S	0.42	0.07	0.41	0.07	0.40	0.07
	Model (2)	0.40	0.06	0.40	0.06	0.41	0.06

^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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