OGM reveals SVs that cause hemophilia at high resolution. For hg38, axes were plotted, indicating the positions of the genes affected by the variants. For each sample, the green bars show the reference sequence chromosome X mapping, and the blue bars show the mapping assembled from the sample's OGM data. Vertical lines on the bars represent the positions of the labels between the hg38 and study sample maps, which are connected by gray lines. The nucleotides listed are not necessarily those of the actual breakpoints but rather indicate the extent of the fragments, as determined by the positions of the labeled DNA motifs within the variant regions and closest to the chromosomal breakpoints. (A) In a sample from patient 1, a deletion region of up to 451 kb was found in Xq27.1. The extent of the deletion is indicated by a red background. The variant caused a complete deletion of F9, MCF2, and one-fifth of ATP11C. (B) Variants in samples from patients 2, 3, and 4 are int22h-related rearrangements. Int22 consists of 3 sets of highly homologous sequences, with int22h-1 located within F8 (indicated by red squares), int22h-2 (indicated by yellow squares), and int22h-3 (indicated by blue squares) located outside the F8 gene. A 567 kb inversion was detected in the Xq28 region in patients 2 and 3, consistent with Inv22 Type I, and patient 3 was an Inv22 carrier. A 94 kb fragment was found in Xq28 of patient 4, which was inverted and repeatedly inserted within F8. MUT, mutated; Ref, reference; WT, wild-type.