Genomic dosage profile of diploid persimmon Kunshenshi KK family

To test a method for CNV analysis we worked on a diploid and biparental pedigree consisting of a family of persimmon trees, the Kunshenshi (KK) family of diploid Diospyros lotus, which are comparable to a mammalian family, and were parented by an XX female and an XY male (Akagi et al. 2014). Short reads from 32 females and 25 males were mapped on the reference genome and read counts in 4153 100kb bins were counted and standardized on a value of 2 (corresponding to 2x genome copies) by dividing by the population mean count. In the resulting table the rows correspond to 100kb genomic bins and the columns to the sequenced persimmon tree.