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Compatibility and incompatibility of fragments. The boxes represent exons, the dotted lines represent implied introns, and the solid lines represent the fragments between pair mates. (A) Compatible single-end reads. (B) Incompatible single-end reads. (C) Compatible paired-end reads. (D) Incompatible paired-end reads. (E) X5 is an uncertain read because it overlaps the intron in Y5 and another different intron in Y6
