Ancestral allele estimates for cattle using est-sfs software with the K2 model

Overview

The assignment of bovine ancestral alleles was based on a model comparison of alleles from cattle with alleles from outgroup species: Water Buffalo, Sheep, and White-Tailed Deer. 

The frequency of cattle alleles are determined using 79 representative individuals from 1000 Bull Genomics Project. We utilized multiple sequence alignments of 110 species (78 ruminants and 32 mammalian outgroup species), available from http://animal.omics.pro/code/index.php/RGD/loadByGet?address[]=RGD/Download/comSynDownload.php, to determine the alleles in Water Buffalo, Sheep, and White-Tailed Deer at each locus.

We employed the est-sfs software with the K2 model to infer the probability (Pancs) of the major allele in cattle being ancestral. Alleles were determined to be ancestral if they were the major allele at a site with Pancs > 0.8 or the minor allele at a site with Pancs < 0.2.

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The columns of this dataframe are

chrome: chromosome index.

pos: physical location of SNV.

cattle_ref: reference allele of cattle.

cattle_alt: alternative allele of cattle.

cattle_maj:  major allele of cattle.

water_buffalo: the sequence of water_buffalo.

sheep: the sequence of sheep.

white_tailed_deer: the sequence of white_tailed_deer.

p_maj_anc: the probability of the major allele of cattle being ancestral.

ancestral_allele: the inferred ancestral allele.