Figure 3.

Schematic of the parameters to assess junctions in SpliceMap. The deep green reads are uniquely mapped supporting reads (nUM = 4) and the wheat reads are multiply mapped supporting reads. Thus, nR of this junction is 6. But some supporting reads are redundant, so nNR = 4. There are four and three uniquely mapped reads (grey green) in upstream and downstream adjacent regions of 40 nt respectively, so nUP = 4 and nDOWN = 3.