Supplemental Material for Vandenplas, Calus, and Gorjanc, 2018

Supplemental figures are available in File S1. A description of the simulated genotype and phenotype datasets for each scenario is provided in File S2. Simulated genotype and phenotype datasets for the 5 replicates of each scenario are provided in Files S3, S4, and S5

MOESM1 of Assigning breed origin to alleles in crossbred animals

Additional file 1. Table S1: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a BC crossbred animal for the chromosome 1. Results are averages (SD) across the 10 replicates. Table S2: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a BC crossbred animal for the chromosome 2. Results are averages (SD) across the 10 replicates. Table S3: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a A(BC) crossbred animal for chromosome 1. Results are averages (SD) across the 10 replicates. Table S4: Percentages of alleles correctly assigned a breed origin (%correct), incorrectly assigned (%incorrect), or unassigned (%unknown) for a A(BC) crossbred animal for chromosome 2. Results are averages (SD) across the 10 replicates. Table S5: Percentages of BC and A(BC) animals having at least 80 % of assigned alleles, and Spearman rank correlations between the order of the phasing analyses obtained from the forward selection and a predefined order of the same phasing analyses for the A(BC) animals, with a relaxation factor equal to 10 %. Results are averages (SD) across the 10 replicates. Table S6: Percentages of assigned alleles of the chromosomes SSC2 and SSC18 for an EF or a D(EF) animal, and percentages of EF and D(EF) animals having at least 80 % of assigned alleles, with a relaxation factor equal to 10 %. Table S7: Average (SD) percentages of assigned alleles of the chromosomes SSC2 and SSC18 for an EF or a D(EF) animal. Table S8: Percentages of alleles correctly assigned a breed origin (%correct) and incorrectly assigned (%incorrect), for the chromosome 2 with 9 phasing analyses with, or without, the additional rules. Results are averages (SD) across the 10 replicates