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Base Undercalls

Read1      ACCCAG
Read2      ACCCAG
Read3      ACCCAG
Read4      ACC*AG
Read5      ACCCAG
Consensus  ACCCAG

In the above case we see that Read4 has a C missing. Once again we must check the traces to be sure that we wish to edit the reading. If so, then we can either make an edit specifically to Read4 itself (in "replace" mode) or type C in the consensus at this column. The latter will change either the base type of the * in Read4 to c, or will change it's confidence value to 0. This depends upon the value of the "Edit by base type"/"Edit by confidence" setting in the Edit Modes menu.

When replacing base types, it is preferable to use lowercase letters. This makes the modified base stand out. However even when using uppercase letters it is always possible to search for edits at a later stage, although they won't be as obvious to the human eye. Finally, note that the "Allow replace in cons" mode must be set to to enable this solution.


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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_69.html