Fig. 7
From: JBrowse 2: a modular genome browser with views of synteny and structural variation
A An alignments track showing SKBR3 PacBio alignments, with a large (> 1000 bp) insertion highlighted by soft-clipped reads in blue (1) and a smaller insertion in purple (2). B The “Read vs ref” view created by right-clicking a read in the Alignments Track creates a Linear Synteny View comparing the read vs the reference genome, which allows you to see the inserted non-reference bases easily. Users can also select regions on the read or reference sequence and select “Get sequence” (3)