Sample to Sample Comparison pane
The Sample to Sample Comparison (top) pane for the Comparison viewer is a correlation table, that, by default, displays the percentage of major alleles that are shared among all the project samples, with the Jaccard Index measurement used to calculate the comparison. Diagonal cells in the correlation table compare a sample to itself and by default, are highlighted in black. All other cells in the correlation table compare one sample to another for the proportion of shared variants. By default, these cells are highlighted in a blue color gradient from 0 to 100%, where 0% cells are blank/white and 100% cells are the darkest blue in the gradient. The Proportion of Shared Variants, which is a read-only legend that is located above the pane, shows this gradient.
 | You can change the default highlighting colors that are used in the Sample to Sample Comparison pane. See To edit the Comparison viewer variant highlighting colors. |
The following options are available for the Sample to Sample Comparison pane.
• Save As: You can click the Save As option that is displayed above the Comparison pane to open the Save Sample to Sample Comparison As dialog box and save the information that is displayed in the pane as text (.txt) file with a filename of your choosing. By default, the text file is saved in the same directory as the project, but you can always select a different location.
• Column variant type and Row variant type: You can change the variant types that are used for calculating the correlation (Major, Minor, or Both). You can select the same or different variant types for the column and the row.
 | You can also use the options that are available on the Comparison viewer main menu (Major to Major, Major to Minor, and Minor to Minor) to quickly reset the variant types that are used for the calculation of the correlation. |
• Show Percentage: Selected by default. Shows the percentage of shared variants for the samples that are being compared. If you clear this option, then the absolute number of shared variants is shown instead.
• Use Jacquard Index. Selected by default. The Jaccard Index measurement is used for the calculation, which results in the variant values in either the row or the column being used in the divisor. If you clear this option, then a Simple measurement is used for the calculation, which results in only the variant value in the column being used in the divisor.
As you change any of the options for the correlation calculation, both the correlation table display and the correlation calculation are updated accordingly. You can hold your mouse pointer over any entry in the correlation table to open a tooltip that displays the percentage or absolute number of matched variants, and if applicable, all the variants that are unique to each appropriate sample.