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).

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