Table 1. Insertion location, integration site in soybean genome and 5’ and 3’ Flanking Junction reads by whole genome sequencing of TE1 and TE2 single and TE1 x TE2 breeding stack events.
| Trait | Breeding Generation and Sample Number | Integration site in soybean genome | Total Reads | Reads mapped to genome (Coverage) | Reads mapped to Transgene (Coverage) | Number of Junction Pair End (PE) pairs | 5’ Junction Reads coverage | 3’ Junction Reads coverage |
|---|---|---|---|---|---|---|---|---|
| TE 1 | F2-1 | Gm06:18,552,249..18,556,606 | 98,725,411 | 93,762,230 (10X)* | 863 (9X)** | 72 | 6**** | 5 |
| TE 1 | T3-3 | Gm06:18,552,249..18,556,606 | 119,386,991 | 110,949,911 (11X) | 938 (9X) | 72 | 8 | 6 |
| TE 2 | F2-10 | Gm02:10,027,285..10,027,342 | 108,314,430 | 102,156,087 (10X) | 517 (4X)*** | 29 | 1 | 2 |
| TE 2 | T3-1 | Gm02:10,027,285..10,027,342 | 95,660,998 | 91,367,370 (9X) | 952 (8X) | 47 | 4 | 5 |
| TE 1 in TE 1 x TE2 stack | Single generation | Gm06:18,552,249..18,556,606 | 146,746,063 | 140,544,330 (14X) | 1,128 (11X) | 38 | 8 | 3 |
| TE 2 in TE 1 x TE 2 stack | Single generation | Gm02:10,027,285..10,027,342 | 146,746,063 | 140,544,330 (14X) | 1,338 (11X) | 13 | 6 | 5 |
* The coverage of the genome was calculated by the formula [(number of reads)*length of a read]/genome size] with an average read length and the size of the soybean genome being equal to 100 bp and 975,000,000 bp, respectively.
**The coverage of the T-DNA was calculated by the formula [(number of reads)*length of a read]/length of T-DNA] with the insert size of ~10,000 bp in Trait 1 and ~12,500 bp in Trait 2.
***The coverage of the T-DNA in TE2 in F2 generation is half of that in T3 generation as the sample (F2-10) representing the former is in hemizygous state.
**** The coverage within the junctions was represented by number of reads spanning those regions.