1. A method for identifying genetic mutations in an organism by comparative genomic resequencing, the method comprising the steps of: a) hybridizing a reference genome to a first microarray set to produce a reference intensity pattern, the first hybridization set tiling the genome of the organism; b) hybridizing a test genome to the same microarray set to produce a test intensity pattern; c) comparing the differences between the reference and the test intensity patterns to generate a mutation map which indicate possible locations of nucleotide differences between the reference and test genomes; and d) resequencing the mapped mutations on a second microarray set to identify with specificity the nucleotide differences in the test genome as compared to the reference genome.