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Program to count Phred 20 bases

Phillip San Miguel pmiguel at purdue.edu
Fri Oct 15 04:07:15 EST 1999


Is there a publically available program or script that will
count the number of Phred 20 bases (that is, the number of
bases with quality scores of 20 or higher) for each sequence
in a quality file generated by Phred?

I have a couple of other questions about Phred: what are the
scores generated by the -qr and how is a "High Quality Base"
defined?  I've noticed that Phred will generate a histogram
of scores of some sort using the -qr qualifier. What are
these scores?  They do not appear to be the number of  bases
with Phred scores greater than 20 nor do they appear to
correspond to the number of high quality bases. And what is
a "high quality base" anyway. I get this score using the
-trim "" qualifier in Phred, but what is it?

Phillip San Miguel




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