Table 4 SVs distinguishing donor from recipient—Filtering and cross-validation
ClassAll SVsa/Filtered SVsbTransforming SVs (≥1)c
DeletesdInsertseTotalfDeletesdInsertseTotalf
1 bp277 / 166318 / 203595 / 369434689
2−10 bp192 / 154180 / 148369 / 300332961
11−100 bp53 / 3463 / 5195 / 6851214
101−1000 bp39 / 3334 / 3090 / 734512
>1000 bp23 / 2130 / 1862 / 485410
Complexg100
Total584 / 408625 / 4501221 / 8689096186
  • SVs, structural variants; IGV, Integrative Genomics Viewer.

  • a Total SVs from a Mauve alignment. Indel directionality is relative to transformation, such that insertions are donor-specific and deletions are recipient-specific. Reporting indels is complicated by “insertional deletions,” where donor sequences would replace recipient sequences (17% of filtered SVs), a pattern more common for large SVs (44% affecting >100 bp), so net change is reported.

  • b Subset of indels for which reads distinguished donor from recipient and <5% of genotypes were ambiguous.

  • c Subset of SVs with the donor allele present in ≥1 of the 72 selected clones.

  • d SVs with indicated number of bps would be deleted by transformation; the net deletion (i.e., the donor allele was shorter than the recipient allele).

  • e SVs with indicated number of bps would be inserted by transformation; the net insertion (i.e., the donor allele was longer than the recipient allele).

  • f SVs affecting the indicated number of bps; sum of donor and recipient allele lengths.

  • g Complex SVs (inversions, relocations, etc.) missed by the genotyping method but manually inspected using IGV.