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.
One or more contigs can be displayed and are drawn in the same order
at the input contig list (which need not necessarily be in the same order as
the contig selector). 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.
![[picture]](consistency_p.unix.gif.html)
(Click for full size image)
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Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_34.html