Supplemental data to publication "evidence of rare misassemblies in the bovine reference genome revealed by population genetic metrics" (animal genetics)

Abstract: Population genetic metrics help to evaluate the genomic map coordinates of the SNP markers sited on SNP genotyping arrays. A three-step approach combining the recombination and linkage disequilibrium (LD) analyses was applied to the Illumina Bovine SNP50 genotyping array in a large pedigree of Holstein cattle consisting of 367,056 animals distributed in 1,053 half-sib families to investigate if the markers fit into the assigned physical map coordinates. A panel of 65 markers was suggested as misplacement candidates. Results of both recombination and LD analyses for each candidate marker are presented. List of marker names and coordinates within 30 refined problematic regions are supplemented. This data is associated with a publication in Animal Genetics (Qanbari et al. 2022).