i am trying to calculate mean Phred scores for my sequencing data, but i feel not very comfortable about it. There are actually two ways of calculating. (I just use an existing sample) giving: 3 reads with a mean phred score of 20, 10 and 3 (meaning Error rates of 1%, 10% and 50%, respectively)
Way 1 to calculate: Just take the arithmetic mean of the q scores:
(20+10+3)/3 = 11
Way 2: Take the arithmetic mean of the error rates:
(0,5+0,1+0,01)/3 ~= 0.2
And then calculate the q score by
-10*log10(0.2) = 6.99
The Author of this Blog claims, that Way 2 is the correct version, but i still do not get why.
Is somebody able to answer this question?
Thanks a lot