Additional file 1: Table S1. of Identification and validation of risk loci for osteochondrosis in standardbreds

Named genes located within the top regions of association on ECA14 from the GWA analysis. Table S2. Haplotype analysis within the top regions of association on ECA14 from the GWA analysis. Table S3. Top GWA SNPs from GEMMA mixed model analysis of data imputed to 670 k and 2 M SNP lists. Table S4. Summary of variants by type and region. Table S5. Regions of interest for which detailed annotation of SNPs was performed. Table S6. Putative risk variants for OC that were selected for inclusion in the custom Sequenom genotyping assay (n = 240). Table S7. Frequency of alternate allele in cases and controls for each SNP in the Sequenom platform that genotyped successfully in the discovery or validation populations. (DOCX 93 kb

Probability, random processes, and ergodic properties

In this new edition of this classic text, much of the material has been rearranged and revised for pedagogical reasons. Many classic inequalities and proofs are now incorporated into the text, and many citations have been added

Additional file 11: Figure S3. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

MNEc2M Inter-SNP distance and informativeness by breed. Distance between SNPs on the MNEc2M array were calculated by breed group (See Additional file 5: Table S5) at various minor allele frequency cutoffs (0, 0.01, 0.03, 0.05, 0.10). Breed groups with asterisk (*) indicate a combination of studbook breeds. (PNG 1152 kb

Additional file 1: Table S1. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Whole genome sequencing (WGS) samples. Whole genome sequencing samples with horse identification and read depth. 153 Individuals representing 24 breeds (Twilight is included as 4 entries). Table includes horse identifier, breed, contributing laboratory and coverage statistics for each individual in both the nuclear and mitochondrial genomes. Variant calling groups indicate which individuals were grouped together during variant discovery. (XLSX 21 kb

Additional file 2: Table S2. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

SNP50 breed informativeness. Impact of breed on SNP50 informativeness. Table shows informativeness (MAF ≥ 0.05) of the legacy, SNP50 SNP set for light, draft, and pony breeds described by McCue et al. [1, 2]. Mean number of informative SNPs per breed was ~42,000 (~77%). 19,427 SNPs were informative in all 14 breeds. (XLSX 8 kb

Additional file 5: Table S5. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Sample breed and tagging breed groups. Samples (n = 485) from either whole genome sequence (WGS) or from the 2M test array (SNP) were assigned to one of 15 tagging breed groups based on their reported breed. (XLSX 21 kb