A spanning pair is 1 paired-end read with discordant alignments. A split read is a read that contains the fusion point, with the segments separated by the fusion point mapped to different genes. The green and red long rectangles represent the reference sequences of gene1 and gene2, while the green and red arrows represent reads or segments mapped to gene1 and gene2, respectively.
Liu et al. BMC Bioinformatics 2013 14:193 doi:10.1186/1471-2105-14-193