Ancestral alleles of cattle defined through population-based likelihood ratio test

Ancestral alleles are useful in the identification of genomic regions under selection also known as signature of selection. However, the available list of ancestral alleles in cattle to date particularly at whole genome sequence level are not comprehensive. We present a list of 70 million ancestral alleles (combining autosomal and X chromosomes) on the cattle genome defined using likelihood ratio test. \nLineage: Ancestral alleles were determined by comparing the allele (of biallelic site) in cattle to the alleles of orthologous positions of the seven out-species (bison, Banteng, domestic yak, Gayal, Gaur, Kouprey and wild yak) using the population-based likelihood ratio test. The allele with a higher likelihood ratio in out-species group was defined as the ancestral alleles for the genomic position. In addition, the probability of an allele being ancestral was estimated as the proportion of the likelihood ratio of an allele to the sum of the likelihood ratios of the two alleles at a locus. Further, the number of out-species supporting the ancestral alleles at a genomic position is provided as additional measure for confidence for ancestrality.