Loss of UPF2 leads to increased AS-NMD. (a) Proportions of regulated canonical junctions versus junctions supporting AS events (red, upregulated; yellow, unregulated; green, downregulated), with additional distribution pie charts underneath displaying the predicted percentage of PTC+ junctions versus PTC- junctions (junctions that do not elicit a PTC) of upregulated junctions (black, PTC+; grey, PTC-). (b) The number of AS junctions and the number of PTC+ junctions are shown as a function of number of junctions per gene in the top and bottom panels, respectively. The slopes of the curves were calculated by linear interpolation. In total, our pipeline detected 10,061 unique AS junctions in BMMs (8,107 in WT and 9,447 in KO) compared to 33,164 in the liver (25,390 in WT and 31,041 in KO), and calculations in the table (top) show the number of unique AS junctions per million mapped reads for each sample. No minimum read cutoff was used in (b).