Gap4 - Quality

Plotting Consensus Quality

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

(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.

Examining the Quality Plot

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.

: +Strand -Strand
a: Good Good (in agreement)
b: Good Bad
c: Bad Good
d: Good None
e: None Good
f: Bad Bad
g: Bad None
h: None Bad
i: Good Good (disagree)
j: None None

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 ]

This page is maintained by staden-package. Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_39.html