Fig. 4

Rep-68 Under-representation. Histograms showing the results of CDUR applied to the AAV2 Rep-68 gene using the gc3 shuffle method. In each graph, the filled black bars represent the “below” portion, that is, the number of shuffled sequences with that given metric below that of the one computed for the input. The red line shows the Normal distribution approximation given the mean and standard deviation (SD) from that calculation. a The mutation motif counting graph (belowTAC). The observed number of TAC mutation motifs is 20 (which includes the GTA mutation motifs on the bottom strand). The black bars are all shuffled sequences with fewer observed mutation motifs than our input. b The replacement transition graph (RepTr_belowTAC), also shown with the Normal approximation. c The replacement transition fraction graph (RepTrFrac_belowTAC). Our sequence had an observed RepTrFrac of 0.25, so the sequences with a lower RepTrFrac are filled in with black (see Table 2 for complete results)