Random perturbation results. Comparison of the RSEM-EVAL score of the ground truth assembly to those of randomly perturbed versions of that assembly. (A) Changes in the relative scores of the perturbed assemblies with increasing mutation strength. For each class of perturbed assemblies, we computed the mean percentage change in the normalized RSEM-EVAL score for the 1,000 randomly perturbed assemblies in that class. The normalized RSEM-EVAL score is the RSEM-EVAL score of the assembly minus the RSEM-EVAL score one would obtain for the null assembly with no contigs and is useful when positive scores are necessary. For each mutation type, the normalized RSEM-EVAL score is plotted as a function of the mutation strength, with error bars corresponding to 95% confidence intervals. (B) RSEM-EVAL error rates for each perturbed assembly class. Error bars correspond to the 95% confidence intervals for the mean error rates.