Table 4 Functional annotation of the detected InDel variants in three Philippine mango species

3 prime UTR truncation

1

3 prime UTR variant

6,098

5,528

4,744

10,397

9,645

8,874

5 prime UTR truncation

3

3

2

3

5 prime UTR variant

3,913

3,489

2,987

6,417

5,935

5,265

Bidirectional gene fusion

3

1

1

5

2

4

Conservative inframe deletion

708

579

550

587

489

502

Conservative inframe insertion

796

746

643

664

637

564

Disruptive inframe deletion

1,266

1,086

1,026

1,114

947

907

Disruptive inframe insertion

842

706

682

743

692

669

Downstream gene variant

299,752

273,125

225,389

244,707

228,871

194,277

Exon loss variant

4

3

5

3

4

Frameshift variant

7,571

6,757

6,054

5,307

4,857

4,371

Intergenic region

422,962

380,721

318,804

369,574

338,484

296,065

Intragenic variant

2

4

4

21

21

17

Intron variant

83,767

75,690

65,064

123,064

114,750

102,061

Non-coding transcript variant

118

98

74

267

209

184

Splice acceptor variant

151

147

129

229

221

177

Splice donor variant

252

187

178

287

244

240

Splice region variant

2,412

2,078

1,851

2,815

2,647

2,375

Start lost

112

108

90

104

94

93

Start retained variant

11

9

7

9

8

12

Stop gained

242

212

188

198

192

170

Stop lost

96

80

88

75

76

70

Stop retained variant

11

13

8

11

12

13

Upstream gene variant

335,143

307,696

249,591

275,331

258,779

215,457