Table 5 SNP annotation

Total SNP count in annotated genes

15,752

27,123

24,906

24,909

26,504

19,308

21,040

28,962

24,518

48,792

23,669

Average read depth per SNP

13

17

15

14

20

12

15

21

15

-

16

Total length of annotated transcripts covered (in nt)

49,680,448

54,713,084

53,001,316

49,673,932

57,245,339

49,901,790

55,367,363

51,984,636

51,682,304

SNPs overlapping with dbSNP

12,748

22,182

20,494

20,380

21,741

15,598

17,082

23,828

20,048

39,998

19,345

SNPs in annotated exons

14,271

23,757

22,450

22,311

23,202

17,023

18,333

25,381

21,544

43,283

20,919

SNPs in annotated UTRs

4,156

7,226

6,659

6,657

6,939

5,082

5,533

7,644

6,479

12,748

6,264

SNPs in annotated CDS

10,115

16,531

15,791

15,654

16,263

11,941

12,800

17,737

15,065

30,535

14,655

Non-synonymous SNPs

4,759

7,814

7,441

7,338

7,769

5,704

6,113

8,383

7,271

14,372

6,955

Synonymous SNPs

5,365

8,731

8,366

8,329

8,512

6,250

6,704

9,372

7,808

16,196

7,715

SNPs eliminating start codons

6

11

9

8

8

7

7

12

6

17

9

SNPs causing premature termination codons

29

70

68

67

80

44

44

72

55

125

59

SNPs eliminating termination codons

24

28

29

31

30

21

23

29

28

49

27

SNPs in splice sites

220

369

342

323

354

245

254

357

313

606

309

SNPs in annotated introns

2,120

4,483

3,469

3,609

4,377

3,036

3,575

4,752

3,957

7,488

3,709