Extended Data Figure 9.

Representation of alignments in path buffers. The “Virtual Alignment Forest” is a more detailed version of the one in Fig. 1a. Pink edges mark paths that were pruned out due to lower probability in order to maintain the tree structure. Shaded backgrounds mark paths that have not been pruned out and are therefore represented in path buffers, and darker shading indicates that part of the path is represented in multiple buffers. “Path Buffers” store cumulative log probabilities that can be used to compute a rolling mean log probability as mapping progresses, as well as “stay” versus “move” events represented by dotted versus solid lines. Seed mappings are inferred from the FM index coordinate which are also stored in the buffers.