Characteristics of observed junctions.

As described in the main text, we split the observed junctions into five classes based on gene model databases. For each class, we present the number of such junctions, the average number of reads spanning each junction in that class, the percentage of the junctions observed in any tissue assayed in Wang et al. [2], the percentage of 5′ and 3′ splice sites of each junction that fall near an annotated splice site (“near” here is defined as within 50 base pairs), and the percentage of the 5′ and 3′ splice sites of each junction that show strong evidence of evolutionary conservation (defined as a mean phyloP score [31] at the two canonical bases of the splice site).