Percentage of heterogeneity for SNPs in high and low confidence regions. 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. Regions that Quiver identified as being supported and those flagged as having low support were examined separately and were found to have similar profiles. While the HGAP2 consensus typically contained the base supported by the majority of reads, there are regions where 100% of the reads mapping to the assembly support an alternative call.