Showing posts with label sanger. Show all posts
Showing posts with label sanger. Show all posts

Monday, September 5, 2011

Phred Quality Score

Phred quality score is the standard quality score to determine the quality of a base calling.
Q = -10 log p
where,
Q = phred quality score
log is base 10.
p = probability that the base call is incorrect. Therefore, the smaller the p, the higher the Q.

Since p is the probability that the base call is incorrect, therefore we can view (1-p) as the correctness as well. If p = 0.01, then the probability that it is correct is 0.99 (i.e. 99% correct). This corresponds to Q = 20.

Q=20 ==> 99% accuracy
Q=30 ==> 99.9% accuracy
Q=40 ==> 99.99% accuracy

There is another variant of quality score, i.e. Solexa quality score which is generated from the Solexa pipeline (Illumina prior to version 1.3).