This tar file includes the bowtie2 index for the mouse genome build GRCm38. We use the UCSC mm10 version of the genome, corresponsing to GRCm38/GCA_000001635.2, including the 22 assembled chromosomes (1-19, X, Y, M), the 22 unplaced contigs, and the 22 unlocalized contigs, but excluding any alternative sequences. This is the same reference as used by the ENCODE Consortium for data processing: https://www.encodeproject.org/data-standards/reference-sequences/ .