The present invention is an improved method of resequencing DNA using microarrays to rapidly map and identify SNPs, deletions and amplification events present in the genome of an organism. The method is performed by hybridizing a reference and a test genome to two separate arrays with each array exhibiting a specific intensity pattern. The intensity differences between the reference and the test genome arrays are used to produce a mutation map. The mapped differences are resequenced on a set of resequencing arrays to identify specific genetic mutations.
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