Table 1 Sequence exchange events defined from whole genome skim sequencing. Detailing for the 12 Paragon × Chinese Spring samples skim sequenced; the sample number, CO and frequency defined using the 35K array, % of these events validated by skim sequencing, GCs identified with track lengths > 40,000,000 bp (representative of COs), > 20,000,000 bp, > 500,000 bp, 10,000–500,000 bp, 2000–10,000 bp, and 20–2000 bp. High-confidence GCs are defined as those where the specific array SNP allele that was used to make the call could be validated in the skim sequencing
Sample | CO frequency (35K array) | % of array COs validated by skim seq | GC frequency (35K array) | % array GC positions validated with skim sequence | % GC-specific SNP alleles validated with skim sequence | Track length > 40 Mbp | Track length > 20 Mbp | Track length > 500 kbp | High-confidence track length > 500 kbp | Track length 10–500 kbp | High-confidence track length 10–500 kbp | Track length 2–10 kbp | High-confidence track length 2–10 kbp | Track length 20 bp–2 kbp | High-confidence track length 20 bp–2 kbp |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0055 | 73 | 86.3 | 429 | 96.0 | 83.9 | 56 | 94 | 186 | 177 | 2884 | 898 | 4230 | 1158 | 15,262 | 5676 |
0334 | 70 | 91.4 | 507 | 96.8 | 86.9 | 55 | 88 | 337 | 321 | 10,017 | 8155 | 7687 | 4828 | 18,913 | 9543 |
0200 | 54 | 87.0 | 461 | 92.8 | 82.6 | 53 | 81 | 200 | 184 | 3433 | 1322 | 5251 | 1691 | 19,602 | 8609 |
0270 | 54 | 81.5 | 483 | 96.7 | 50.9 | 79 | 122 | 278 | 257 | 2907 | 1694 | 3721 | 1853 | 17,651 | 11,383 |
0008 | 65 | 98.5 | 413 | 94.2 | 85.2 | 43 | 72 | 215 | 197 | 3588 | 1630 | 5954 | 2508 | 26,063 | 13,451 |
0119 | 69 | 91.3 | 409 | 94.4 | 82.8 | 43 | 75 | 330 | 317 | 5926 | 3995 | 6097 | 2898 | 20,600 | 9961 |
0005 | 55 | 94.5 | 363 | 96.7 | 84.6 | 51 | 79 | 238 | 213 | 4303 | 2228 | 6002 | 2402 | 22,553 | 10,738 |
0018 | 52 | 92.3 | 386 | 94.3 | 87.0 | 58 | 101 | 241 | 218 | 2531 | 1148 | 4323 | 1773 | 18,583 | 10,225 |
0097 | 53 | 98.1 | 322 | 96.3 | 86.9 | 30 | 56 | 177 | 163 | 4296 | 1717 | 7203 | 2694 | 28,299 | 13,193 |
0004 | 34 | 88.2 | 378 | 97.9 | 86.6 | 47 | 73 | 217 | 202 | 3377 | 1701 | 5242 | 2206 | 20,889 | 10,829 |
0010 | 37 | 100 | 319 | 94.7 | 89.1 | 44 | 85 | 309 | 291 | 3292 | 1383 | 4926 | 1860 | 22,063 | 11,234 |
0281 | 39 | 79.5 | 306 | 97.7 | 89.4 | 66 | 102 | 212 | 196 | 2642 | 1097 | 3426 | 1195 | 13,612 | 5930 |