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Fraction of perfectly mapped, part correctly mapped and incorrectly mapped reads for simulated unspliced (A) and spliced (B) reads of simulation 1 and 2, respectively. “CM Bwt1”, “CM Bwt2”, “CM Bwa” denote ContextMap 2 used with Bowtie, Bowtie 2, and BWA as underlying alignment program, respectively. If a gene annotation was provided, “ann” was added to the name of the respective program.
