Fig. 1

Palindrome death. a Schematic representation of the reference sequence for P8 and its surrounding regions. The inverted orange arrows show P8, with the VCY genes indicated by blue boxes. The remaining colored arrows represent sections of the flanking sequences that facilitate interpretations of the rearranged structures shown in other figures. b Representative fiber-FISH image of HG000096, showing the reference sequence for palindrome P8 and its surrounding regions. Seven PCR probes (1–7) together with the BAC clone RP11-53 K10 (blue) produce the fiber-FISH signals shown schematically above the fiber-FISH image. c Corresponding fiber-FISH image for HG00742 carrying a deletion of one P8 arm and the central spacer and lacking one red and green signal. d Representation of the location of the deleted section on the reference sequence (top) and resulting deleted structure (bottom). The small arrows show the location of the breakpoint PCR fragment. e 10x Linked-Read sequencing results represented as a Loupe file. The green axes show the read depth, and the intensity of the heat-map the extent of barcode sharing. Read depth is reduced across P8 due to deletion of the region between the black arrows and dispersal of the remaining reads across both palindrome arms. f Breakpoint PCR showing amplification in the deleted sample HG00742, but not in HG03006 with the reference structure. g Sanger sequence of the breakpoint showing (top) two regions of the reference sequence with nucleotides present in the breakpoint sequence shown in upper case blue and nucleotides absent in lower case black; (center) the sequence trace; and (bottom) nucleotides matching the reference sequence in upper case blue and novel nucleotides in lower case orange