These are diagrams produced during the annotate step. These represent the putative fusion events of a single breakpoint pair.
If the draw_fusions_only flag is set to False then all events will produce a diagram, even anti-sense fusions
MAVIS supports generating diagrams of all transcripts for a given gene. These can be overlaid with markers and bam_file pileup data. This is particularly useful for visualizing splice site mutations.
The above diagram was generated using the overlay command
mavis overlay RB1 \ -o /path/to/output/dir \ --read_depth_plot rna /path/to/bam/file \ --marker M1 48939029 \ --annotations /path/to/mavis/annotations/reference/file