Threshold determination for the scaffolding of 454 contigs by Illumina MPs. The number of bridging MPs per gap was normalized to the total number of all gap bridging MPs per BAC (x-axis) and counted in bins of 0.02 (y-axis, logarithmic). An exponential relationship is observed for bins 0.02-0.44 (red line). The first bin (≤0.02) deviates from this relationship, most likely due to weakly supported false positive bridgings. Therefore, only contig pairings >0.02 were considered for scaffolding.