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Table 3 Summary of annotation variants for four traits

From: Genome-wide association studies of yield-related traits in high-latitude japonica rice

Traits

DH

PH

PW

TI

number of SNPs

25

25

223

44

number of variants

27

26

229

46

number of effects

81

64

589

133

chromosome

4, 6, 7, 11

1, 3–8, 10–12

1–12

1–12

3′ UTR variant

–

–

3

–

5′ UTR variant

2

–

1

–

downstream gene variant

29

19

170

38

frameshift variant

–

–

1

–

intergenic region

16

18

143

31

intron variant

11

2

33

10

missense variant

1

3

19

4

splice region variant

–

–

1

–

stop gained

–

–

1

–

synonymous variant

–

3

31

4

upstream gene variant

22

19

187

46