MOESM1 of A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle

Additional file 1. Additional information describing the design of the GGP-F250 assay [15, 46–50]. Table S1. Number of variants present on the GGP-F250 assay for each of the design waves. Description: The wave refers to the order in which candidate variants were selected to be added to the manifest in order to use 250 K beads. Designed: number of variants present in the manifest submitted for synthesis, Final Manifest: number of variants in the final delivered manifest, Failed Synthesis: number of variants that failed oligo synthesis, Filtered: number of variants that passed filtering based on automated and/or manual clustering using 18,684 individuals, Final List: number of variants in the final marker list that were used to produce genotypes, Variable: number of variants with at least one alternate allele observed in 18,684 individuals. Table S2. Description of abbreviations used in Table S1 as filtering criteria. Table S3. Animals by breed used to develop the Illumina cluster file for genotyping. Removed denotes samples that were excluded from clustering due to low call rate. Table S4. Genotype reproducibility for samples genotyped twice. Variation in the total number of compared genotypes is due to the individual sample call rates on each assay.