in Roche 454 pyrosequencing [11], although, overall the quality scores decrease more rapidly for inserted (error) bases. Counter intuitively, it is possible for the first base in a homopolymer run to have lower quality score than later bases, irrespective of whether the homopolymer is the correct length or not (Figure S10). This could originate from penalties for local or environmental noise (P1 and P6 in the documentation), which allow individual base qualities to be adjusted if immediately upstream or downstream calls are noisy.
