Not imputed) genotypes in the genome sequence derived dataset (70 SNPs from the Illumina BovineHD chip), giving an indication of the accuracy of variant calls derived from the RNA seq alignments. Although some residual signal remained, this appeared to be dispersed over the broader locus, and may have represented population stratification incompletely accounted for in the pedigree based models, and/or valid association signal from other genes. Wang et al.3 reported mapping of a milk fat percentage QTL of large effect in German Holstein Friesian cattle using the Illumina BovineSNP50 chip, locating to a similar position to that reported here.
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