Fig. 1

Long-range haplotype characterization of rDNA in the C57BL/6J strain. A Schematic of rDNA in the C57BL/6J mouse strain. Adapted from Refs [2] and [35]. B rDNA coding unit haplotypes in a C57BL/6J MEF line defined using ultra-long-read Nanopore sequencing. The top track shows representative read depth from C57BL/6J kidney short-read whole-genome sequencing data, and locations of SNVs cross-validated with Nanopore data. The bottom track shows only SNVs that distinguish rDNA haplotypes. Bold contour denotes variants unique to that specific haplotype. Bars with non-muted colors and no contour indicate positions associated with the A/C haplogroups defined by the variant at position -104. Bolded positions in the x-axis (9005, 12376) are variants within the 28S rRNA and present in mature ribosomes. Haplotypes are denoted by three letters, for the variant nucleotides at positions -104, 8063, and 12736, respectively. 12736 distinguishes the 2 haplotypes with “A” at -104, 8063 distinguishes the 2 haplotypes with “C” at -104 (see Additional file 3: Fig. S2). Although these three positions combined robustly identify the haplotypes, each individual position is not strictly haplotype-specific. C Co-localization analysis of rDNA haplotypes in MEF. For Nanopore reads spanning multiple rDNA units, each cell shows the average proportion of units assigned to the corresponding column haplotype in a read, given that the read includes at least one unit of the haplotype indicated in its row