A novel deletion detected on chromosome 01 in transgenic plant WPT_384-1-1. Figure S2. A novel deletion on chromosome 19 in transgenic plant WPT_391-1-6. Figure S3. Test for intracultivar variation in the parental lines by genotyping 47 individuals taken from GRIN stocks of the varieties ‘Bert’ and ‘Williams 82’. Figure S4. Genotyping diverse lines including the 41 SoyNAM parents, cultivars ‘Archer’, ‘Minsoy’, and ‘Noir1’, ‘Bert-MN-01’, and ‘Wm82-ISU-01,’ for previous evidence of SV found in transformed plants. Figure S5. Novel deletion on chromosome 11 in transgenic plant WPT_389-2-2. Figure S6. Novel duplication on chromosome 13 in transgenic plant WPT_301-3-13. Figure S7. Southern blot analysis of HindIII digested genomic DNA. Figure S8. Microhomology of sequences at the T-DNA left border and the sites of genomic integration for three transgenic plants. Figure S9. Structure of the heterozygous transgene insertion on chromosome 05 in transgenic plant WPT_391-1-6. Figure S10. Transgene insertion on chromosome 13 in transgenic plant WPT_389-2-2. Figure S11. Pipeline for utilizing resequencing data in this study. (PPTX 3058 kb)