Near isogeneic lines developed from residual heterozygosity have been critical to genome science in inbred crops. They have been used for fine map development, positional cloning, proteome analyses and QTL confirmation. Regions showing either higher or lower rates of recombination have been detected. Regions where heterozygosity remains long after it should have been fixed are known. Here a pair of F5:7:16 NILs were analyzed with 52,000 SNPs using Illumna technology. Heterozygosity was detected at a 10 fold lower frequency than heterogeneity. Genomic features associated with increased hetrozygosity included members of the resistance gene families. Recombination rates varied across a 20 fold range by chromosome and by regions of chromosomes. The mean distance between recombination events was just 100 kbp. Genomic features associated with increased recombination included members of the helicase gene family. Near isogenic lines were shown to be more powerful tools than expected for genomic analyses.