Phase block tracks

If the session contains phased variant analysis data, a phase block track can be applied to the Analysis view. A phase block track shows quality or confidence score for the phasing calls. The track is a graphical representation of the Phase Block column in the Variants view.

For detailed information about applying tracks, see Work with Tracks. To add white space above and/or below the tracks, use the sliders in the Layout section.

If you apply both a phase block track and an alignment track, you may notice that the phase blocks do not line up exactly with the alignment rows of the same color. Why not? Phasing is calculated by assigning reads in the assembly to one allele (usually a parent) or the other. This is done by finding sites in the genome where there are two or more populations and then correlating the read assignments with one another. Phase blocks, on the other hand, are defined as the region between two heterozygous sites where the algorithm can confidently assign heterozygous sites to one of the alleles. This means that when there aren’t additional heterozygous sites, reads can extend beyond the ends of phase blocks.

To change Phase block track options:

Select a Phase blocks track in the Tracks panel and then click the Options tab to expand the Options section.

• By default, phase blocks are shown in alternating colors of medium green and blue. To change a color, click on the corresponding color box and make a selection from the color chooser.

• If you want to show all phase blocks in the same color, rather than in alternating colors, uncheck the Alternate color box.