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

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

Total

25,632

18,390

14,333

15,713

6,678

5,504

5,915

4,101

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

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