Illustrated example 3 - rrwick/Verticall GitHub Wiki

This page illustrates the Verticall pairwise process using a real pair of assemblies:

• A388: an Acinetobacter baumannii isolate from Greece
• A83: an Acinetobacter baumannii isolate from Australia

Unlike in the previous two examples, these are fragmented Illumina-only assemblies.

Here is the distance distribution with the smoothing and partitioning shown:

These two genomes are very closely related in the vertically-inherited parts of their genomes - the majority of the sliding windows have zero differences. So most of the distribution's mass is pushed up against the left side.

There is horizontal content in this distribution, but you have to zoom way down on the y-axis to see it:

Here is A388, the first assembly:

And here is A83, the second assembly:

You may have noticed that the contig painting was a bit more lined up in example 1 and example 2 than it is here. That's because the previous two examples were done with completed assemblies that had consistent starting positions, while this example's assemblies are made of short-read contigs.

The mean distance between these two isolates (using the entirety of their alignments) is 0.00304. This is similar to the value you'd get using Mash (distance=0.00406) or FastANI (identity=99.667%, distance=0.00333).

However, that distance includes the horizontally-acquired regions, so if we want the vertical distance (i.e. the distance using only the vertically-inherited parts of the genome), it will be too high. Verticall's mean vertical distance only uses the vertically-painted parts of the alignments and gives a much lower distance of 0.00006.