Example of assigning coverage evenness scores to candidate junctions. Reads that align to a candidate new junction sequence may start at many different positions relative to the breakpoint. Reads that do not unambiguously support the new junction (gray arrows) because they do not extend across the breakpoint and any overlap or read-only bases (yellow highlighting) are not counted toward the evenness score. Although the two examples have the same number of reads that support the new junction because they align across the breakpoint and match the junction better than the reference genome (black arrows), the example in (a) is well-supported because these reads start in many different registers with respect to the breakpoint as would be expected for a normal reference genome location, whereas the example in (b) has reads beginning at a small number of biased positions with respect to the junction. This coverage evenness score is used to calculate a skew p-value to accept or reject a candidate junction, after also accounting for differences in the maximum number of read start positions that can support each candidate junction. In cases of tandem duplications much shorter than the read length, reads must also extend several “continuation” bases past any unique-only or overlap sequence to count as supporting a junction, as illustrated in Figure 5.