Variants tracks

If you are viewing an assembly created in SeqMan NGen, you can add a Variants track to the Analysis view using the method described in Work with Tracks. In contrast to the Alignment track, which lets you see variants at the level of individual bases, the Variants track is a “bird’s-eye view” of variants in context of the overall alignment.

To display this track, open the Tracks panel and check one or more of the boxes to the left of Analysis body > Variants > (sample names).

Notes about variants tracks:

• You may need to use the green horizontal zoom slider to see the variants clearly.

• To resize the track vertically, use the slider that appears if you hover over the bottom middle of the track data. You can also resize the track and change the amount of white space above/below the track using sliders in the Layout section.

• The styles used to represent each type of variant are controlled by choices made in the Variants section of the Style panel.
  
  

• For phased assemblies, the Variants track uses bifurcations at each phase block to delineate variants in each of the two alleles (parents). To best visualize phased assemblies, we recommend using this track in conjunction with the Alignment and Phase block tracks. The following image shows these three tracks together, with the Variants track at the bottom.