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).