Figure 1

The probe level data of one SNP. (A) Left: The SNP has 20 probe pairs, whose normalized intensity values in one array are displayed and connected in blue (perfect match or PM) and gray (mismatch or MM) lines. The probe set has probe pairs for both A and B alleles and for the forward and reverse DNA strand. Right: The same probes are displayed in a brightness scale, with the matching A and B probe pairs in the same column. The SNP genotype is called as AB in this sample. (B) The probe data of the same SNP in another sample with genotype AA. (C) The probe data of the SNP in a third sample with genotype AA. However, the probe signals here are about one half as those in B, presumably corresponding to hemizygous deletion at this SNP position.