Table 3 Functional annotation of the detected SNP variants in three Philippine mango species

3 prime UTR variant

34,712

26,993

21,424

58,036

46,735

36,749

5 prime UTR premature start codon gain variant

3,076

2,351

1,821

4,850

3,751

2,897

5 prime UTR variant

19,305

14,370

11,386

30,836

24,082

18,839

Downstream gene variant

1,903,377

1,501,470

1,139,595

1,570,171

1,300,734

968,689

Initiator codon variant

30

24

18

32

33

25

Intergenic region

3,033,446

2,310,351

1,862,224

2,801,150

2,196,966

1,811,990

Intragenic variant

104

80

35

Intron variant

528,400

412,723

327,832

823,307

675,164

538,294

Missense variant

125,037

91,959

79,309

111,102

88,532

73,636

Splice acceptor variant

643

494

411

731

580

491

Splice donor variant

545

406

345

711

584

486

Splice region variant

16,351

12,542

10,269

18,521

14,905

12,266

Start lost

302

214

207

183

147

113

Start retained variant

13

9

8

Stop gained

2,601

1,887

1,651

1,630

1,393

1,055

Stop lost

492

339

304

309

231

190

Stop retained variant

191

154

140

143

133

102

Synonymous variant

87,448

63,950

54,816

86,133

66,813

55,417

Upstream gene variant

2,040,834

1,627,526

1,203,524

1,702,492

1,419,809

1,026,224