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Old 11-18-2010, 02:55 PM   #2
Location: Berkeley

Join Date: Nov 2010
Posts: 12

I can see your confusion. There is something very strange about figure 1 in their paper. Panel (b) might make sense if what they were plotting was error rate relative to base position for a 40bp read. How can panel (a) even go up to 41 if the max Illumina quality score is 40 as they themselves state in the text?

Look at these papers for better treatment of the question of quality scores vs error rates:
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