The format of the file is a simple tab-delimited table with 5 columns: chromosome, left_pos, right_pos, line1 (lower coverage), line2 (higher coverage). Each row represents a region defined by the interval from left_pos to right_pos on chromosome for which line1 and line2 are very similar in their SNP calls (based on the DGRP FASTA files). The line with lower coverage was masked. See the manuscript linked above for details. This table results in Figure 1 in the manuscript.