The recombinant progeny of a genetic cross between monomorphic ChrIa harboring strain ME49 and divergent ChrIa harboring strain VAND were whole genome sequenced using Illumina method in order to generate a more detailed genetic map. These sequence information has been used to develop fine genetic map, and to understand copy number variations (CNV), duplication, crossover and double crossover points. Whole genome sequences from these recombinant clones were utilized to understand the role of monomorphic ChrIa for fitness advantage.