Categories of gene-overlapping SVs. The top shows gene structure, including transcribe start site (array), 5 '-UTR (light grey), start codon (red), coding sequence (blue), stop codon (yellow), 3 '-UTR (dark grey), intron and intergenic region (thin black line). A total of 15 categories were defined, including whole gene DEL (WlGnDel), DUP (WlGnDup), and INV (WlGnInv), predicted loss-of-function (pLoF) when DEL or MEI occurred in CDS, copy gain (CpGn) when DUP occurred in CDS, coding INV (codInv), coding BND (codBnd), 5 ' Regulation (5 ' Rglt), and 3 ' Regulation (3 ' Rglt). CDS-mapped SVs were defined as weak (Wk) impact if mapped CDS counts less than 20% of its own length. In contrast, it had a strong (St) impact. Similarly, UTR-mapped SVs were defined as weak (Wk) impacts if mapped UTR lengths were less than 20% of their own lengths. In the bottom part of this panel, we defined the relationships between SVs and genomics features like eQTL, sQTL, promoter, and enhancer as overlapped if they were localized in SVs or flanking if they were localized in 5-kb flanking regions of an SV on both sides.
