Array-based polymorphism mapping at single nucleotide resolution

A method of assessing the location of one or more polymorphisms in a first genome, relative to a corresponding reference genome, the method comprising:

• i) contacting, under hybridizing conditions, fragments of the first genome with a plurality of polynucleotide probes, wherein the probes are completely complementary to different, but overlapping, portions of the reference genome;
• ii) assessing the hybridization intensity for each of the probes with the fragments;
• iii) for each of a plurality of genomic locations which are overlapped by multiple probes:
• a) for each probe that overlaps the location, comparing the assessed hybridization intensity with the predicted hybridization intensity, wherein the predicted hybridization intensity for each probe is calculated based on hybridization intensity of fragments of the reference genome with the probes;
• and
• b) combining the comparisons for each probe to yield an estimate that the polymorphism occurs at the location;
• and
• iv) comparing the estimates to identify where, within the overlapping portions, a polymorphism occurs, whereby the polymorphism is predicted to occur at the nucleotide residue for which the estimate is highest.