Assembly comparison by gene mapping. (a) Number of RefSeq mRNA sequences (out of 8,689) that can be aligned to each genome assembly at varying coverage cutoffs (horizontal axis) with at least 95% sequence identity. (b) Difference in the number of mRNAs mapping to the two assemblies at different levels of coverage, plotted as UMD2 minus BCM4. Negative values indicate that BCM4 has more genes at a given level, while positive values indicate that UMD2 has more. For example, at 0-5% coverage, 104 more mRNAs map to BCM4 than to UMD2. At 95-100% coverage, 275 more mRNAs map to UMD2. Blue, UMD2 assembly; red, BCM4 assembly.