Examples of SNP data. A) Typical clustering of satisfactory data for POPA SNP 3_0004; red cluster area = homozygous AA, blue = homozygous BB, green dots within purple cluster area are 1:1 mixtures of parental DNA for three DH mapping populations. One germplasm sample (black dot) was outside of any call cluster and was thus scored "no call". B) Typical theta compressed data for POPA SNP 3_1104; although the polymorphism can be mapped in an individual population there are often wrong calls in such data and the cluster separation is problematic for general use in germplasm analyses or with multiple mapping populations; set to Gentrain 0.000, 100% "no call". C) Typical vertically separated clusters for POPA SNP 3_0070; generally polymorphic for a different locus than the source of the targeted SNP, which results in wrong annotation and degraded synteny; set to Gentrain 0.000, 100% "no call". D) Data for POPA SNP 1_1166 (ABC07305-1-4-322) from the OWB population; two DH samples behave as heterozygotes (purple cluster), far from the homozygotes (red = AA; blue = BB), instead with the 1:1 mixture of parental DNAs (green dot in purple cluster).