Blacklist regions are tightly distributed across the chromosome and sequester high read mapping signals. (a) Distribution of mapped reads along human chromosome 1 in hg19. (b) An example blacklisted region on chromosome 1. Displayed are pre-filtered ENCODE ChIP-seq peak calls, quantile normalized median read signal (Reads), and quantile normalized median multimapped read signal (Multi). Axes are scaled for illustrative purposes and signal values are truncated at approximately 10-fold enrichment. Signal in these regions are up to 6400× background levels. (c) An example “normal” ENCODE ChIP-seq peak region on chromosome 1 selected as a region containing ChIP-seq peaks.