RH locus landscape and breakpoint sequencing. The representative introns and exons are shown as lines and boxes below the coordinate axis, respectively; the arrow on the last exon represents the genic orientation. RH boxes are shown as purple boxes below the axis. Twenty-nine heterozygous SNV markers were developed from HiFi cluster reads and involved in assembling and phasing haplotypes of this locus (strings in each gray box give the genomic coordinate, reference to alternative alleles of corresponding SNV marker). (A) Nineteen amplicons were designed to target the whole region of this locus and identify breakpoints therein (amplicons are shown as brownish red bars above the axis, and the recognized nonhomologous end-joining breakpoints and homologous recombination breakpoint regions are marked in lime and magenta/red, respectively). (B) The breakpoint of CE8-CE3 fusion tested via Sanger sequencing (inversion intervals are shown as arrows above the base pairs).