Figure 3

Sequencing reads alignment to two reference genomes, C2T and G2A reference genomes. Due to the pointer size limitation by the Bowtie program, reads alignment needs to be performed using the two reference genomes separately. Cross check and comparison are made subsequently to remove reads not uniquely aligned. At the end, sets A and C are read pairs aligned to C2T reference genome, while sets B and D are read pairs aligned to the G2A reference genome.