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Introduction

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 that 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

[picture]
(Click for full size image)

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.

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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_83.html