Fig. 2
From: Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions
Results of the WGS and linked-read WGS analysis from patient P1.2. A Varbank2 implemented conifer CNV analysis tool showing results from the WGS dataset. Z-scores from patient P1.2 in cyan-coloured bars and also as extrapolated curve. Affected region is indicated by the black horizontal bar. Genes in this region are indicated by purple horizontal bars. The markers (probes throughout the exons) are evenly distributed among the positional X-axis. The black curves represent the control collective, consisting of a fixed set of samples for the given enrichment kit. B Linked-read Loupe browser v.2.1.1 haplotype resolved SV results for patient P1.2 compared to a control sample (matrix view). Genomic region chr1:16.023.378-16.077.660 (hg38) is displayed on y- and x-axis for both alleles, respectively. Number of reads is indicated by green vertical bars. Sequence coverage (barcode overlap) is indicated by the heat map ranging from zero coverage (white) to high coverage (black). C Xdrop indirect sequence capture and ONT long-read sequencing results for patient P1.2 [26]. Gene-specific nucleotides are indicated by red background; breakpoint regions are indicated by grey background. Long stretches of homologous genomic DNA sequence have been shortened, indicated by […]. D Reconstruction of the genomic structural rearrangement of patient P1.2. The three breakpoint regions result in a rearrangement of fragment B and fragment C and the deletion of the genomic DNA in between these fragments. Genomic DNA Fragments were rearranged according to the identified breakpoints. New genomic rearrangement consisting of fragment A-C-B-D. The common sequence transposition haplotype equates to the transposition of fragment C. Genes are indicated in blue with exons as blue vertical bars. Gene orientation is indicated by blue arrows. Colour coding of genomic fragments A (green), B (orange), C (blue), and D (red). Genomic sequence coordinates refer to the hg38 human reference. †Linked-read control carries the CLCNKA 3′ UTR sequence transposition haplotype heterozygously