Profile of Mu insertion sites detected by MuSeq.

1Insertions that have reads in all 48 grid samples include endogenous Mu elements in the W22 inbred genome that are common to all plants in the population as well as insertions inherited from founder lines that are distributed widely enough within the UniformMu population to be represented in every row and column in the grid.
2Germinal insertions that are shared by two or more maize lines in the grid are detected in multlple samples, including both axes, but do not appear in all samples. Because the number of possible locations in the grid that are consistent with multiple pairs of axis coordinates is in general larger than the number of actual locations of the insertion, these insertions cannot be unambiguously assigned to maize lines using 2D Mu-seq data alone.
3Germinal insertions that are assigned unique locations in the grid are detected in both axes with reads occurring in a single sample of each axis.
4Insertions due to probable somatic transpositions produce reads in only one axis. For this analysis, insertion sites within this group that were detected by fewer than 5 reads (predominantly singletons) are classified separately to distinguish them from insertion sites that have robust read counts in a single axis.