FANCD2 expression analysis from RNA-seq data for FA18 and FA19 LCL cell lines. (A) Wiggle plot displaying RNA-seq read coverage along with the UCSC FANCD2 gene track (shown below). Data from FA18 and FA19 are shown on top and bottom, respectively. The number of sequence reads (range) is indicated on the y-axis and is reflected by the height of the peak for each exon. The decreased number of sequence reads for exon18 (arrow) is apparent for FA18. This reflects the 4.7-kb genomic deletion that removes this exon. Multiple individual RNA sequence reads from FA19 spanning exons 15 to 17 (blue shade) are displayed in the lower panel (generated using the IGV program). Each horizontal line is an independent sequence. The thicker rectangle at each exon shows the mapped RNA sequences, while the thin line connects the gaps (introns) and connects the sequences from a single read. It is apparent that several sequence reads that include both exon 15 and 17 do not include the sequence for exon 16 (thin line), which is evidence of exon skipping. At the top of each exon, the gray color reflects the number of sequences at single-base resolution. Reduction in the reads for exon 16 compared with the 2 flanking exons is readily apparent. (B) Display of a cross section of RNA-seq (top) and genomic (bottom) sequence read alignments for FA19 in the region spanning the first nucleotide of exon 16 (*) that carries a missense mutation (c.1279G>T; p.V427F). Some of the genomic sequence reads show the heterozygous mutant T allele while RNA-Seq shows no reads with the mutant allele, indicating that the allele carrying the exon 16 mutation is skipped during messenger RNA splicing.