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Examining the 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. Commands available on the data 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 ]

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_84.html