Different granularities of reference-based measures computed by REF-EVAL. (A) The contig-level measure requires at least 99% alignment between a matched contig and reference sequence in a one-to-one mapping between an assembly and the reference. (B) The nucleotide-level measure counts the number of correctly recovered nucleotides without requiring a one-to-one mapping. Unlike the contig-level measure, it gives full credit to the two short contigs. The table on the right gives both the contig-level and nucleotide-level recall values for (A) and (B).