This option can be invoked from the main gap4 View menu, in which case it appears as a single plot, or from the View menu of the Template Display, in which case it will appear as part of the Template Display.
For each base in the consensus a "quality" code is computed based on the accuracy of the data on each strand and whether or not the two strands agree. In a future release it will be renamed the "Strand Comparison Plot" This "quality" is then plotted using colour and height to distinguish the quality codes shown below.
Colour Height Meaning grey 0 to 0 OK on both strands, both agree blue 0 to 1 OK on plus strand only green -1 to 0 OK on minus strand only red -1 to 1 Bad on both strands black -2 to 2 OK on both strands but they disagree
![[picture]](template.quality.unix.gif.html)
(Click for full size image)
For example, in the figure we see that the first four hundred or so bases are mostly only well determined on the forward strand.
Note that when displaying many bases the screen resolution implies that the quality codes for many bases will appear in the same screen pixel. However the use of varying heights ensures that all problematic regions will be visible, even when the problem is only with a single base position. Hence when the quality plot consists of a single grey line all known quality problems have been resolved, at the current consensus and quality cutoffs.
The quality plot appears as "Calculate quality" in the Results Manager window (see section Results Manager).
Within the Results Manager commands available, using the right mouse button, include "Information", which lists a summary of the distribution of quality types to the output window, and "List" which lists the actual quality values for each base to the output window. These quality values are written in a textual form of single letters per base and are listed below.
An example of the output using "Information" and "List" follows.
============================================================
Wed 02 Apr 12:14:06 1997: quality summary
------------------------------------------------------------
Contig xb56b6.s1 (#11)
81.00 OK on both strands and they agree(a)
3.94 OK on plus strand only(b,d)
11.98 OK on minus strand only(c,e)
1.85 Bad on both strands(f,g,h,j)
1.22 OK on both strands but they disagree(i)
============================================================
Wed 02 Apr 12:14:09 1997: quality listing
------------------------------------------------------------
Contig xb56b6.s1 (#11)
10 20 30 40 50 60
eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeehee eeeeeeeeee eeeeeeeeee
70 80 90 100 110 120
eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeeeee
130 140 150 160 170 180
eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeeeee eeeeeeeeee
190 200 210 220 230 240
eeeeeeeeee eeeeeeeeee heeeeeeeee eeeeeeeici iiaiaciiia aaaaaaaaac
250 260 270 280 290 300
aaaacaaaaa aaaaaaaiia aaaaaaaaaa aaaaaaaaaa aaaabaaaaa aaaaaaaaaa
310 320 330 340 350 360
aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa faaaaaaaaa
[ output removed for brevity ]