Species and genome assemblies considered in this study.

aAbbreviated common names used by the 2× Mammals Consortium are listed here. In some cases, different names have been used in the ENCODE project (see Table S1). bUCSC designation. cReported average coverage. dNumber of ENCODE regions for which high-quality sequence is available, or“–” if ENCODE sequence is unavailable. eThe mouse and rat assemblies are considered “essentially complete” but some improvements are still underway (see http://www.ncbi.nlm.nih.gov/genome/assembly/grc/mouse/ and http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat).