Table 3 Distribution of SNPs, types and zygosities of the variants per chromosome in ‘Indo’ and ‘Su Shuai’

chr1

128 340

97,462

68.45%

68.43%

31.55%

31.57%

84.34%

88.27%

15.66%

11.73%

chr2

188 280

156,325

68.59%

68.25%

31.41%

31.75%

74.14%

89.91%

25.86%

10.09%

chr3

174 749

143,473

68.76%

68.41%

31.24%

31.59%

73.93%

92.08%

26.07%

7.92%

chr4

92 896

76,283

67.63%

67.59%

32.37%

32.41%

75.41%

88.97%

24.59%

11.03%

chr5

150 451

95,589

67.62%

67.17%

32.38%

32.83%

84.25%

88.79%

15.75%

11.21%

chr6

129 297

101,624

68.74%

68.74%

31.26%

31.26%

71.46%

91.35%

28.54%

8.65%

chr7

98 294

75,169

68.12%

67.75%

31.88%

32.25%

80.55%

89.80%

19.45%

10.20%

chr8

138 638

103,421

68.60%

68.41%

31.40%

31.59%

75.92%

90.04%

24.08%

9.96%

chr9

147 795

108,343

68.12%

67.63%

31.88%

32.37%

82.87%

88.60%

17.13%

11.40%

chr10

156 277

116,019

67.41%

67.20%

32.59%

32.80%

79.92%

91.05%

20.08%

8.95%

chr11

188 022

138,474

68.08%

67.63%

31.92%

32.37%

82.45%

88.43%

17.55%

11.57%

chr12

167 505

125,460

68.28%

68.06%

31.72%

31.94%

77.87%

92.04%

22.13%

7.96%

chr13

145 527

115,371

68.78%

68.67%

31.22%

31.33%

84.07%

91.24%

15.93%

8.76%

chr14

131 530

93,323

68.60%

68.29%

31.40%

31.71%

80.61%

87.62%

19.39%

12.38%

chr15

204 749

161,391

68.43%

68.37%

31.57%

31.63%

79.31%

88.75%

20.69%

11.25%

chr16

96 988

78,842

68.44%

67.69%

31.56%

32.31%

79.94%

90.44%

20.06%

9.56%

chr17

115 068

87,780

67.67%

67.41%

32.33%

32.59%

77.75%

88.38%

22.25%

11.62%

Total

2 454 406

1,874,349

68.27%

68.02%

31.73%

31.98%

79.09%

89.82%

20.91%

10.18%