Illustration of the four types of simulated fragments. Illustration of the four types of simulated fragments. Type A fragments represents reads that have the first half as upstream noncoding gene regions and the latter half as downstream gene coding regions. Three different types of type B fragments are full coding regions. Type C fragments represent reads that have the first half as downstream gene coding regions and the second have as a post-gene flanking region. Type D fragments represent reads that are fully non-coding regions. The example shown here is for 700 bp reads, and the same scheme of fragmentation is used for all read lengths.