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. 2015 Sep 24;5(11):2257–2266. doi: 10.1534/g3.115.021584

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Copyright © 2015 Cockram et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Allele calling for the two peak Snn1 SNPs in the 90k SNP dataset, using GenomeStudio software. SNPs BS00093078_51 (top) and Excalibur_c21898_1423 (bottom) were classified as dominant and codominant, respectively, following the standard calling procedures. Visual inspection of BS00093078_51 shows clustering of AA homozygotes (red) and AB heterozygotes (purple), ‘no call’ genotypes (black) located between the AA and AB clusters, and an absence of BB genotypes. These ‘no call’ genotypes represent true heterozygotes, based on the observation that both the BB and AB clouds have two sub-clusters.