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(A) After correcting for a large insertion of a mdg1 transposable elements upstream of rpr in strain B6 (brown) the apparent difference in coverage between strains B6 and A4 (green) is largely eliminated. (B) Correcting for the effect of a hopper TE in an intron of Mef2 in the A4 genotype largely eliminates an apparent difference in chromatin configuration.
