Matrix QA Reports

Sample Missingness and Heterozygosity QA Report

This screen will display the Sample Missingness and Heterozygosity Ratios data calculated by the Matrix QA Operation in descending Missingness Ratio order.

Selecting the Sample Info Report node in the tree (1) will display this screen. Specify how many lines you want to see in the report and push the “Get” button (2) to reload the requested rows.

The last two columns in the table shows the Missingness and Heterozygosity Ratios.
Clicking on the “Save” Button will allow you to save the current report view, as well as the total report output if necessary.

Sample Missingness and Heterozygosity QA Plot

Selecting the Sample Heterozygosity Ratio Plot node in the tree (1) will display this screen. The chart (2) is zoomable if you drag a box with the mouse pointer.

A threshold line is drawn as specified on (3) and any sample beyond this threshold will be highlighted. The given threshold will be saved for down-stream filter operations by Sample Heterozygosity. By hovering with the mouse on any point you will see the Sample ID, Heterozygosity and Missingess ratio values. The current view of the chart can be saved to a PNG file and zoom state can be reset at (4).

Marker Missingness QA

This screen will display the Marker Missingness Ratio data calculated by the Matrix QA Operation

Selecting the Marker Missingness Report node in the tree (1) will display this screen. Specify how many lines you want to see in the report and push the “Get” button (2) to reload the requested rows.

The last column in the table shows the Missingness Ratio.
Clicking on the “Save” Button will allow you to save the current report view, as well as the total report output if necessary.