Additional file 1: of Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Minor Allele Frequencies: Full matrix of the MAF for all classes. (XLSX 13 kb

Additional file 2: of Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Euclidean matrix with distance values showing the similarities between functional class GRM. The more similar the GRM is between two classes the lower the Euclidean distance measure is. This is also represented by the color green. The more dissimilar the GRM is between two classes the higher the Euclidean distance measure is. Represented by the red color. (XLSX 10 kb

Additional file 4: of Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Variance Component Analysis 2: performed using variants with MAF thresholds of 0.000000001 and 0.1. For each functional class is the proportion of variance captured by each class, along with the total proportion of variance captured for each trait represented as a percentage, in brackets. (XLSX 11 kb

Additional file 2: of Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Euclidean matrix with distance values showing the similarities between functional class GRM. The more similar the GRM is between two classes the lower the Euclidean distance measure is. This is also represented by the color green. The more dissimilar the GRM is between two classes the higher the Euclidean distance measure is. Represented by the red color. (XLSX 10 kb

Additional file 3: of Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

The heritability for each trait along with the permutated heritability obtained from the permutation test using the same number but randomly chosen SNPs (which was replicated 5 times and significance is determined as greater or less than the average of the proportion of variance explained by the randomly chosen SNP ± 2 × S.E). The heritability percent difference is simply the difference between the class heritability and the permutated heritability multiplied by 100. (XLSX 13 kb

Additional file 5: of Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Variance Component Analysis 2: performed using variants with MAF thresholds of 0.000000001 and 0.1. For each functional class is the variance explained per sequence variant along with the variance component. (XLSX 10 kb