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  1. Incorrect mapping (non-gapped alignment) GTXX r e1 e2 GTXX GTXX AG GTXX GTXX r Correct mapping (spliced alignment) (1) Read r may be incorrectly mapped to the intron between exons e1 and e2. e1 e2 e3 Gene Read mapped e1 e2 e3 Processed pseudogene (2) Here, the read shown in red, which spans a splice junction, can be aligned end-to-end to a processed pseudogene. Read Exon Intron