Figure 3

Sequence characteristics of false positive junctions. Sequence logos of exon and intron sequence bordering splice junctions in (A) annotated GT-AG introns, (B) unannotated GT-AG introns detected that pass filtering, and (C) repeat induced false positives. (D) Cartoon illustrating how false positives arise from repetitive sequence and sequencing error. A transcribed fragment from a region of repetitive sequence is incorporated into a library. A base calling error (in red) produces a read with an “A” instead of a “T” at the indicated position. This incorrect base call induces an incorrect gapped alignment that minimizes sequence mismatches. (E) Illustration of each false positive error type (Table 2).