Back of a Stamp

My notes on the sequence/quality data from Illumina genome analyser.
Phred
Phred is a program that takes the trace files produced by traditional DNA sequencing, calls the bases and assigns a quality value to each called base.
It calculates a score for each base as:

Qphred = -10 x log10(1/$error_prob)

Where $error_prob is the probability of the base call [...]