Whats the difference between Solexas base scores and Phred scores?
Like Phred scores, Solexa’s base scoring scheme is just a way of expressing estimates of sequencing error probability in a convenient form. Many people are familiar with Phred scores, named after the Phred base-calling software developed by Phil Green and coworkers. A Phred score of a base is Q phred =-10 log10(e) where e is the estimated probability of a base being wrong. If a base is estimated to have a 1% chance of being wrong, it gets a Phred score of 20. Phred score=30 corresponds to 0.1% estimated error, 40 to 0.01%, and so on. We wanted a 4-values-per-base scheme because we wanted a scheme that also encodes information on the next most likely base call. After some discussion with James Bonfield at Sanger we came up with the following: Q solexa =10log10(p(X)/(1-p(X)) You will get one positive score – that’s the score of your base call – and three negative scores.
