In spite of a low MAF, the Y581S polymorphism had a highly significant effect on the αs1-CN phenotype in both HOL and multi-breed analyses, with −log 10 ( P ) values of 31 and 21, respectively; these values were higher than those of the top variant in the peaks after filtering for MAF (20 and 15, respectively).
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Within-breed and multi-breed GWAS on imputed whole-genome sequence variants reveal candidate mutations affecting milk protein composition in dairy cattle.
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The sentences
Thus, the fact that peaks were detected only in HOL (close to significance) and multi-breed (significant) analyses could be due to the relatively low MAF for these variants in MON and NOR.