Figure 1. Assessing the cause of gaps in an assembly of 36nt reads.

The predicted number of sequence gaps based on the Lander-Waterman model (+) is presented along with the actual number of sequence gaps in sets of 36nt Illumina reads (○). This was determined by aligning the reads in each set to the reference sequence. The total number of gaps present in Velvet assemblies of the various read sets is also included (•). The numerous additional gaps observed in the assemblies are due to unresolvable repeats (○ vs. •). Additional details can be found in the Supplementary Methods (File S1).