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Farm wise animal genetic kinship matrices as estimated on the basis of genomic relatedness were inferred from common SNPs that were filtered in after the above quality control procedure. The tool used for the estimation was EMMA expedited (EMMAX) (59), with the following command line: emmax-kin-intel64 -v -M 10 farm_genotypes_tped_file -o farm.hBN.kinf.

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