Table 2.
S. l. cera | S. l. cera | S. l. cera | S. l. cera | S. lyc | S. lyc | S. lyc | S. lyc | ||
---|---|---|---|---|---|---|---|---|---|
Accession | Cervil | Plovdiv | LA 1420 | Criollo | Stupicke | Ferum | Levovil | LA 0147 | |
High effect | Total | 937 | 701 | 648 | 572 | 273 | 240 | 220 | 184 |
Splice site acceptor | 109 | 68 | 63 | 50 | 27 | 23 | 25 | 19 | |
Splice site donor | 104 | 70 | 57 | 64 | 18 | 27 | 17 | 14 | |
Stop gained | 409 | 328 | 294 | 244 | 106 | 76 | 69 | 65 | |
Stop lost | 214 | 169 | 170 | 156 | 86 | 81 | 82 | 65 | |
Start lost | 101 | 66 | 64 | 58 | 36 | 33 | 27 | 21 | |
Moderate effect | Total | 25,632 | 18,390 | 14,333 | 15,713 | 6,678 | 5,504 | 5,915 | 4,101 |
Non synonymous coding | |||||||||
Low effect | Total | 19,681 | 13,698 | 9,700 | 12,244 | 4,750 | 3,624 | 4,304 | 2,537 |
Non synonymous start | 18 | 13 | 6 | 17 | 4 | 4 | 6 | 4 | |
Start gained | 388 | 198 | 183 | 263 | 80 | 39 | 77 | 40 | |
Synonymous coding | 19,218 | 13,448 | 9,481 | 11,924 | 4,654 | 3,564 | 4,208 | 2,485 | |
Synonymous stop | 57 | 39 | 30 | 40 | 12 | 17 | 13 | 8 | |
Modifier | Total | 2,349,654 | 1,669,629 | 1,516,290 | 1,231,706 | 439,151 | 366,977 | 323,588 | 233,987 |
Downstream | 395,731 | 269,917 | 214,303 | 226,489 | 92,087 | 70,696 | 63,259 | 54,897 | |
Intergenic | 1,377,524 | 1,019,498 | 1,000,788 | 676,540 | 215,862 | 200,063 | 164,291 | 102,012 | |
Intragenic | 26,634 | 14,937 | 10,911 | 15,335 | 4,212 | 2,974 | 5,292 | 2,319 | |
Intron | 118,329 | 79,698 | 60,972 | 73,234 | 27,095 | 20,573 | 25,094 | 14,524 | |
Upstream | 422,540 | 280,576 | 225,411 | 234,350 | 95,053 | 71,642 | 63,800 | 59,194 | |
UTR 5 Prime | 2,540 | 1,371 | 1,110 | 1,551 | 507 | 280 | 1,383 | 305 | |
UTR 3 Prime | 6,347 | 3,632 | 2,795 | 4,207 | 1,335 | 749 | 469 | 736 |
SNPs were annotated using SNPeff onto the SL2.40 reference genome.