In article <35D9A878.D6FD8720 at TURING.UNICAMP.BR> felipes at TURING.UNICAMP.BR (Felipe Rodrigues da Silva) writes:
>I would like to understand what the "quality values" really mean in
>Staden. In the Phill Green's Phred program, a quality value of 40 means
>one error in ten to the 4 (10,000). Is it the same in Staden?
Yes, if you enable the "confidence" consensus mode (see the main
Options menu). This uses phred scale quality values in sequences and
produces these values for the consensus qualities. The quality values
are used in the computation of the consensus so that we choose the
most likely consensus base.
Note that the "eba" program does not generate phred scaled quality
values.
For more information, see
http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_125.html
James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/
