a) Simulation of wild rat-based SNP discovery experiment. Simulation is based on the discovery of 485 SNPs between wild 1 and BN in 814 Kbp of shotgun sequence. For 408 of those, the wild rat alleles is found back in one or more inbred strains. The relation between generation of randomly distributed 400 bp shotgun reads and estimated number of newly discovered SNPs is plotted. b) Simulation of SNP discovery experiment, using carefully selected (most polymorphic compared to BN) rat strains (SHR, AUG, and WF) or all rat strains, in comparison with wild rat-based SNP discovery. Simulation is based on 539, 304, 292, 287, and 754 SNPs for wild 1, AUG, SHR, WF, and all strains respectively, in 119 Kbp of genotyped sequence.