to the best of my knowledge reads at the start of SOLiD data set also have a higher error rate .. 
I think it might be also due to edge effect. 


On 9 November 2011 21:49, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Wed, Nov 9, 2011 at 12:03 PM, Bob Harris <rsharris@bx.psu.edu> wrote:
> David, in my experience with Illumina sequencing, it looks like the reads at
> the start of a file have a much higher sequencing error rate.
> Bob H

Yes, reads at the start and the end of the file come from the edge of
the Illumina slide, and tend to be of poorer quality that the reads from
the middle.