Table 2 Median and range (in brackets) of genotype consistency rate between truth (WGS-based) and query (WGBS-based) VCF files for the 94 samples in the first batch

1

91.83 [73.33–100.00]

58.82 [16.67–100.00]

 < 2.2 × 10^–16

2

82.76 [60.00–96.30]

57.14 [21.74–89.47]

 < 2.2 × 10^–16

3

85.61 [72.00–96.83]

58.18 [33.33–84.38]

 < 2.2 × 10^–16

4

86.39 [72.02–92.45]

59.26 [43.42–74.77]

 < 2.2 × 10^–16

5

86.15 [75.05–91.96]

59.87 [50.39–68.19]

 < 2.2 × 10^–16

6

81.61 [68.56–85.10]

57.92 [51.74–59.64]

 < 2.2 × 10^–16

7

81.39 [71.01–84.23]

58.20 [51.43–60.50]

 < 2.2 × 10^–16

8

85.57 [77.95–91.30]

60.80 [53.79–69.19]

 < 2.2 × 10^–16

9

86.39 [77.57–89.83]

61.70 [53.44–69.78]

 < 2.2 × 10^–16