Table 4. SVs distinguishing donor from recipient—Filtering and cross-validation.

Class	All SVsa/Filtered SVsb			Transforming SVs (≥1)c
	Deletesd	Insertse	Totalf	Deletesd	Insertse	Totalf
1 bp	277 / 166	318 / 203	595 / 369	43	46	89
2−10 bp	192 / 154	180 / 148	369 / 300	33	29	61
11−100 bp	53 / 34	63 / 51	95 / 68	5	12	14
101−1000 bp	39 / 33	34 / 30	90 / 73	4	5	12
>1000 bp	23 / 21	30 / 18	62 / 48	5	4	10
Complexg			10			0
Total	584 / 408	625 / 450	1221 / 868	90	96	186

SVs, structural variants; IGV, Integrative Genomics Viewer.

^aTotal 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.

^bSubset of indels for which reads distinguished donor from recipient and <5% of genotypes were ambiguous.

^cSubset of SVs with the donor allele present in ≥1 of the 72 selected clones.

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

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

^fSVs affecting the indicated number of bps; sum of donor and recipient allele lengths.

^gComplex SVs (inversions, relocations, etc.) missed by the genotyping method but manually inspected using IGV.