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Quality Plot

[picture]
(Click for full size image)

Selecting the quality plot from the template display view menu displays a horizontal plot as seen above. For each base in the consensus a quality is computed based on the accuracy of data and strand coverage. This information is then plotted in a colour and height specific to its type according to the table 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

For example, in the figure we see that the first two hundred bases are mostly only well determined on the reverse strand. Immediately following this is a small section of double stranded sequence with many disagreements between strands.

Note that when a large number of bases are being displayed the limited screen resolution causes the quality codes for adjacent bases to be drawn as single pixels. However the use of varying heights ensures that all problematic bases will be visible. 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.

To check problems the contig editor can be invoked by double clicking on the middle mouse button. It will appear centred on the base corresponding to the position that was clicked on.

The quality plot appears as "Calculate quality" in the results manager window. Commands available 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_79.html