Figure 1.—

Computational pipeline for indel and transposon polymorphism discovery. A flow chart of the computational steps that were followed for the discovery of indel and transposon polymorphisms is shown on the left (boxes). A breakdown of the number of traces present at the end of each step is shown on the right. The number of indel and transposon polymorphisms identified is listed at the bottom. Note that the numbers are broken down for each of the three populations examined. TSC, the SNP Consortium traces; WGS, whole-genome shotgun traces; WCS, whole-chromosome shotgun traces.