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Table 2 Distribution of the SNP effect per type of effect in the four cherry-type ( S. l. cera ) and four S. lycopersicum (S. lyc) lines

From: Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

   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
  1. SNPs were annotated using SNPeff onto the SL2.40 reference genome.