How can we get summaries of Phred scores for entire sequences?
The most commonly used way to analyze the quality of sequences is to count the bases that have a Phred quality score above a minimum of 20 (“Phred20 scores”) or 30 (“Phred30 scores”). Phred quality scores of 20 correspond to an error probability of 1%; thus, Phred20 scores tell you how many “good” or “high quality” bases are in a given sequence. Our customers can use a Java tool we have developed to do Phred score analyses; for more information, please visit http://www.codoncode.com/interphace/ You can also see Phred20 scores for sequences in the “Quality” column in the project view of CodonCode Aligner.
