Inversions
Inversions are shown as an entire component row colored in red for specific individuals. Inversions still use Arrival and Departure columns the same but their sequence is interpreted as the reverse complement of the listed pangenome sequence. The visualization does not pick which strand to present a set of nodes, but graph construction should place the majority of individuals on the plus strand.
Figure: Top: A best effort MSA of the same 5 sequences with two nested inversions. MSA’s are not ideal for showing inversions (underlined) and it’s impossible to use a pure linear ordering to place the flipped pink and yellow sequences in inverted positions. Bottom: Inversions are red rows in the inverted individuals that run the length of a Component.
Insertions can be inverted although the upstream is still on the left and downstream on the right, the sequence content is interpreted as reverse complement. The node AATTA would be TAATT in the inverted individuals. In this example, we show an inversion (TTAG) nested inside a larger inversion (center 3 Components) in order to show how Schematics handle complex topology in many individuals.