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. 2011 Dec 8;6(12):e28334. doi: 10.1371/journal.pone.0028334

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The three highlighted clusters display the area where the three different genotypes with homozygous allele A (red), heterozygous AB (purple) and homozygous allele B (blue) are called. Allele calls that fall in the lighter colored areas in between or below these areas are set to ‘failed’. Ellipses are used to adjust the position of the allele calling areas. A) Cluster Type 1: Accurate genotype calling of all three genotypes in essentially all 274 maize lines with clearly defined clusters; B) Cluster Type 2: Three clusters with a number of failed samples at the bottom of the analysis plane that are not called; C) Cluster Type 3: Three clusters with a shift towards one side which is indicative for a duplicated locus. Clusters have to be shifted to the left for accurate allele calling; D) Cluster Type 4: Five clusters which are indicative of two simultaneously scored polymorphic loci in a duplicated sequence. Such markers cannot be scored accurately, so they were deleted from the data set.