Figure 3: Aberrant splicing detection and quantification.

(a) Aberrant splicing events (Hochberg corrected P value<0.05) for all fibroblasts. (b) Aberrant splicing events (n=175) in undiagnosed patients (n=48) grouped by their splicing category after manual inspection. (c) CLPP Sashimi plot of exon skipping and truncation events in CLPP-affected and CLPP-unaffected fibroblasts (red and orange, respectively). The RNA coverage is given as the log₁₀ RPKM-value and the number of split reads spanning the given intron is indicated on the exon-connecting lines. At the bottom the gene model of the RefSeq annotation is depicted and the aberrantly spliced exon is coloured in red. (d) Same as in c for TIMMDC1. At the bottom the newly created exon is depicted in red within the RefSeq annotation track. (e) Coverage tracks (light red) for patients #35791, #66744, and #91324 based on RNA and WGS. For patient #91324 only WGS is available. The homozygous SNV c.596+2146A>G is present in all coverage tracks (vertical orange bar). The top tracks show the genomic annotation: genomic position on chromosome 3, DNA sequence, amino acid translation (grey, stop codon in red), the RefSeq gene model (blue line), the predominant additional exon of TIMMDC1 (blue rectangle) and the SNV annotation of the 1000 Genomes Project (each black bar represents one variant). (f) Per cent spliced in (Ψ) distribution for different splicing classes and genes. Top: histogram of the genome-wide distribution of the 3′ and 5′ Ψ-values based on all reads over all samples. Middle: The shaded horizontal bars represent the densities (black for high density) of the background, weak and strong splicing class, respectively (Methods section). Bottom: Ψ-values of the predominant donor and acceptor splice sites of genes with private splice sites (that is, found predominant in at most two samples) computed over all other samples.