Example RMSD plot. This plot compares 3 Solexa sequenced samples against a Sanger sequenced reference. The blue, green, and red glyphs represent samples from the 1st, 5th and 10th passages, respectively, of the coronavirus. The genomic position is on the x-axis, and the y-axis represents the RMSD distance from each sample to the reference. The M and B annotated dashed lines represent the maximum and biallelic RMSD levels, 0.632 and 0.316 respectively, explained in Figures 4 and 5.