Fig. 5

Comparisons between ploidy, UR width, and UR depth. For these analyses the URs identified in both biological replicate experiments were used. a Number of URs called in a tissue versus its average ploidy value. b For each UR in each tissue, the probe with the minimum log₂ ratio was determined. The probe to the left of the minimum with half the minimum log₂ ratio was set as the left half-min position. The probe to the right of the minimum with half the minimum log₂ ratio was set as the right half-min position. The distance between the left and right half-min positions was determined as the half-min width. The half-min widths or maximum fold underreplication values for a given UR were averaged across biological replicates within a tissue. c Box plots of the maximum fold underreplication of the URs identified in each tissue. “+” denotes the mean value of the distribution. d Box plots of the half-minimum widths of the URs identified in each tissue. “+” denotes the mean value of the distribution. e Maximum fold underreplication versus half-min width for each UR identified in each tissue. The dotted line denotes the fold underreplication cutoff value for calling URs for that tissue. Open circles show URs in pericentromeric regions. Box plot and scatterplots are displayed with log₂ axes