Fig. 2

Comparison of fosmid insert and fosmid-pool scaffold size distributions. Fosmid clone insert size estimates (black contiguous line) were obtained by mapping fosmid end sequences to our merged fosmid pool (FP) assembly. The fosmid end sequencing of only 155,000 unique clones resulted in a very high sequencing depth, so we set a lower threshold of 100 x for the number of times a given length was seen and counted each length only once. While this procedure results in underestimating the amplitude of the density peak, both the shape of the distribution and the mean insert size (36.7 kb) should be unaffected, while the standard deviation is likely an overestimate. The distribution of scaffold lengths from the 96 fosmid pool assemblies is given by the blue dashed line (scaffolds smaller than 2.5 kb were discarded to avoid noise)