We first obtained a noise data matrix using all scattered ("noise") genes excluded by the tight clustering algorithm [ 3].
To identify the fewest number of reference positions required in order to obtain a comparable matrix to a matrix using all available SNPs, a subsampling method was employed.
A relationship matrix constructed using all markers without trait-specific weighting is equivalent to the G matrix in GBLUP, the so-called realized relationship matrix, and is identical for all traits.
GRM is a genomic relationship matrix calculated using all autosomal SNPs with a MAF > 0.05.
Both matrices were generated using all 33,957 SNPs with a MAF ≥3%.
Otherwise, the noise coherence matrix is estimated using all detected noise-only frames, cf. (9).
For running the mixed linear model, a kinship matrix was generated using all SNP markers sites containing no heterozygous calls.
A correlation matrix was generated using all variables to guide the analysis.
Each matrix was run using all carcasses with space and time data.
