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Table 1 Summary of the SNPs and InDels in chloroplast genome of 358 Asian rice and 54 wild rice

From: Signatures of differential selection in chloroplast genome between japonica and indica

Groups

Number of Accessions

Primary

High-quality

Number of variants

Ts/Tv

Number of variants

Ts/Tv

SNPs

InDels

Total

SNPs

InDels

Total

Wild rice

54

2836

966

3802

1.772

1162

212

1374

1.741

Cultivated

Indica

66

105

101

206

0.764

43

24

67

1.688

Te_Japonica

253

75

86

161

0.531

17

15

32

1.125

Tr_Japonica

25

61

77

138

0.488

11

9

20

0.833

Aus

9

97

100

197

0.831

44

25

69

1.588

Aromatic

2

64

79

143

0.524

13

9

22

1.167

Admixture

3

62

75

137

0.512

12

9

21

1.000

Total

412

2867

976

3843

1.767

1172

156

1389

1.751

  1. Notes: Ts/Tv is the proportion of transition/transversion. Te_Japonica: temperate japonica; Tr_japonica: tropical japonica. Primary: All chloroplast genome variants in our studies. High-quality: High quality variants in chloroplast. Here, we removed 80% of missing data and minor allele frequency (MAF) < 0.01