Table 1.

Characteristics of SNP sets obtained by three different protocols; percentage (%) was calculated in relation to the total number of SNPs

Protocol	Number of SNPs	Number of homozygous SNPs (all genotypes homozygous)	Effects predicted by VEP (Ensembl Plants)					Percentage of SNPs with High, Low, or Moderate effects
			HIGH	LOW	MODERATE	MODIFIER	Number of genes with predicted SNP effect
RNA-seq	2295	1055 (46.0%)	56 (2.54%)	745 (33.82%)	744 (33.77%)	658 (29.87%)	1059	70.13
50k Chip	1017	611 (60.1%)	14 (1.42%)	180 (18.24%)	156 (15.81%)	637 (64.54%)	560	35.46
GBS	2806	1865 (66.5%)	23 (0.83%)	393 (14.24%)	366 (13.27%)	1977 (71.66%)	1268	28.34