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Introduction to the Consistency Display

The Consistency Display provides plots designed to highlight potential problems in contigs. It is invoked from the main gap4 View menu by selecting any of its plots. Once a plot has been displayed, any of the other types of consistency plot can be displayed within the same frame from the View menu of the Consistency Display.

An example showing the Confidence Values Graph and the corresponding Reading Coverage Histogram, Read-Pair Coverage Histogram and Strand Coverage is shown below.

(Click for full size image)

If more than one contig is displayed, the contigs are drawn immediately after one another but are staggered in the y direction.

The ruler ticks can be turned on or off from the View menu of the consistency display. The plots can be enlarged or reduced using the standard zooming mechanism.See section Zooming.

The crosshair toggle button controls whether the crosshair is visible. This is shown as a black vertical and horizontal line. The position of the crosshair is shown in the 3 boxes to the right of the crosshair toggle. The first box indicates the cursor position in the current contig. The second box indicates the overall position of the cursor in the consensus. The last box shows the y position of the crosshair. (see section Consistency Display).

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