Supplemental data to publication "Evidence of Rare Misassemblies in the Bovine Reference Genome Revealed by Population Genetic Metrics" (Animal Genetics)

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).

群体遗传指标可用于评估锚定在SNP基因分型芯片上的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）标记的基因组图谱坐标。本研究采用结合重组分析与连锁不平衡（Linkage Disequilibrium，LD）分析的三步研究策略，以包含1053个半同胞家系、共计367056头个体的大型荷斯坦奶牛系谱为研究对象，对因美纳（Illumina）牛SNP50基因分型芯片开展分析，以验证上述标记是否匹配其预设的物理图谱坐标。最终筛选得到65个标记作为定位偏差候选位点。本数据集提供了所有候选标记的重组分析与LD分析结果，并补充了经优化修正后的30个异常区域内的标记名称及对应坐标列表。本数据集关联发表于《动物遗传学》（Animal Genetics）的研究论文（Qanbari等，2022）。