Additional File 4.

Non-random distribution of sequencing error across sequencing clusters. Random cluster generation results in a wide range of inter-cluster distances, causing sequencing error to be non-randomly distributed across clusters. The fraction of reads with two errors is not equal to the squared fraction of reads with one error. Shown are the observed rates for reads with 1 to 5 errors for different Illumina Genome Analyzer data sets (solid lines) presented as test data sets for the Ibis base caller (Kircher et al: Genome Biology 2009) and the expected rates when extrapolating from the fraction of molecules with one error (dashed line).

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Kircher et al. BMC Genomics 2011 12:382   doi:10.1186/1471-2164-12-382