Six SNP quality classes (A) and four variance filters (B) applied to the
genotype class. A. Default SNP quality classes produced by the Axiom Best Practices Genotyping Workflow. B. An example cluster plot for a SNP identified with each of the four variance filters used including: AB.varY identified large heterozygous cluster variance in the Y dimension; AA.varY for homozygous (AA) variance in the Y dimension; BB.varY, for homozygous (BB) variance in the Y dimension; and AB.varX, for heterozygous variance in the X dimension.