Comparison of genotyping using different subsets of probes and multiple analysis methods.

aThe B>M or M>B (all) refers to all probes with a FDR<0.05 in a comparison of B73 and Mo17.
bThe B>M or M>B (2-FC) probes refers to the subset of polymorphic probes that have a FDR<0.0001 and a minimum of 2-fold change between B73 and Mo17.
cThe % calls is the percent of SFPs that could be assigned a genotype using an analysis method.
dThe % consistent refers to the percentage of polymorphic probes that were assigned the same genotype in previously generated genotyping data.
eThe opposing calls are those for which the same probe was assigned different genotypes in different replicates.