Percentage of heterogeneity for SNPs in multiple assemblies. Histograms are presented for the percent heterogeneity of SNPs. Since the population is not intentionally inbred, mixed levels of polymorphism are expected at a variety of positions. A SNP was defined as a position with >20× coverage that had polymorphisms supported by >3 reads. While one might anticipate minimal or no positions at >50% heterogeneity, numerous such instances are observed for all of the assemblers tested with all datasets, including the assemblies based solely on the same Illumina data that was used for the mappings. HGAP2 performed similar to, or better than, the other assemblers examined.