Supplementary Figure 6: Complex, Faeder-specific deletions and rearrangements in the genomic region encoding the transmembrane signaling receptor PLCG2.

(a) Read mapping from a representative faeder individual sequenced at 80× (viewed in IGV) to a 100-kb region of the independent reference genome showing blocks with haploid (40×), diploid, triploid and tetraploid coverage. The predicted intron-exon structures of PLCG2 and three downstream genes are shown, and the predicted effects of deletions (see panel c) on exon retention are indicated. (b) Cartoon of the 100-kb region illustrating coverage, SNP patterns in each block and read-pair mappings that define rearrangements in the region. (c) Model of the Faeder PLCG2 region, consistent with the genomic evidence, and its origin through deletion and tandem duplication. Deletion of block B deletes exon 17, encoding the SH3 domain of PLCG2, and deletion of blocks D3 and E deletes exons 24–26 of PLCG2. Deletion of block Y6 deletes the first exon of gene 18877. Deletion of block Y4 (shared with Satellite) and of block Y2 has no effect on the predicted coding sequences. In the model, the relative timing of the Y2, Y4 and Y6 deletions is not resolved.