Coloring Schema Selection
There are several options available in the Coloring Schema panel. By default, the genome present in Persephone selected from the drop-down list in the upper left corner of the SNPs tab will be used as the reference genome sequence (the Reference genome radio button will be checked by default).
The schematic image of the selected chromosome and genotypes shows SNPs using different colors depending on the Coloring Schema. By default, the Reference genome schema is used: homozygous SNPs identical to the reference genome are blue, homozygous SNPs different from the reference are red, and heterozygous SNPs are green.
The reference can be changed by selecting other coloring schemas. For example, to use one of the genotypes as the reference, select one line in the data grid and drag it to the (Drop parent 1 here) button and select the Referenced genotype radio button. To use both parents drag a second line in the data grid to the (Drop parent 2 here) and select the Two parents radio button.
The lines in the genotype grid can be sorted by values in different columns. If necessary, these values can be used for defining the background of each sub-track, which is done by selecting one of the radio buttons below the data grid. If there are six (6) or less distinct values in the column, a set of predefined colors will be used. Otherwise, the color will be chosen from a gradient spanning over all values of the property.
Clicking the rectangle displaying genotypes at the bottom of the window will bring the selected chromosome into the Maps tab for a more detailed and interactive view of SNPs.