Fig. 2. PhenoSV workflow to assess the impacts of all major types of SVs.

a PhenoSV dissects a given SV that is deletion or duplications into a sequence of genomic segments. The last feature dimensions of genomic segments within the SV region are encoded as 0 for deletions, 1 for duplications, and 0.5 for those outside the SV region. b An insertion is treated as a 100 bp deletion. Displayed are a coding insertion directly disrupting gene C, and a noncoding insertion disrupting a regulatory element that indirectly affects gene A, B, and C. c Inversion type 1 (one breakpoint within genes): we only consider the impacts of its 5’ breakpoint as a deletion truncating the gene C. Inversion type 2 (two breakpoints within genes): we consider impacts of both 5’ breakpoint and 3’ breakpoint as two deletions truncating the gene C and the gene F. Inversion type 3 (no breakpoint within genes): we consider the impacts of both 5’ breakpoint and 3’ breakpoint as a 100 bp deletion centered at the 5’ breakpoint indirectly affecting genes A, B, and C, and a 100 bp deletion centered at the 3’ breakpoint indirectly affecting genes D, E, and F. d Displayed are translocations swapping two genome segments. Impacts of both 5’ and 3’ breakpoints of translocations are considered. Translocation type 1 (gene truncation): the 5’ breakpoint is treated as a deletion truncating the 3’ side of gene C. The 3’ breakpoint is treated as a deletion losing a segment of intergenic region that can indirectly affect the gene F. Translocation type 2 (gene fusion): this resulted fusion gene C–F is treated as a deletion truncating the 3’ side gene C (decreased copy number of the segment) and a duplication of the 5’ side of gene F (increased copy number of the segment). Translocation type 3 (gene truncation): the 5’ breakpoint is treated as a deletion truncating the 3’ side genome region of the breakpoint and indirectly affect genes A, B, and C. The 3’ breakpoint is treated as a deletion truncating the 5’ of the gene F.