Here, we define the ENCODE blacklist- a comprehensive set of regions
in the human, mouse, worm, and fly genomes that have anomalous,
unstructured, or high signal in next-generation sequencing experiments
independent of cell line or experiment.
There's not yet a blacklist available for each species or even each version of mouse/human. You can get the mm9 blacklist here. The equivalent for hg19 is here. There's no equivalent for hg38 and I'm not sure that lifting things over will work, though you could certainly try. We have an mm10 version of this, but I don't know that it's publicly available.