Table 3 Median and range (in brackets) of genotype consistency rate between truth (WGS-based) and query (WGBS-based) VCF files for the 240 samples in the second batch

1

91.55 [73.33–100.00]

59.09 [13.33–100.00]

 < 2.2 × 10^–16

2

82.14 [53.13–97.14]

56.00 [0.00–95.45]

 < 2.2 × 10^–16

3

85.07 [61.70–96.97]

58.00 [26.00–86.96]

 < 2.2 × 10^–16

4

85.71 [72.09–92.52]

59.29 [42.70–76.83]

 < 2.2 × 10^–16

5

86.32 [74.56–91.48]

60.30 [50.16–72.95]

 < 2.2 × 10^–16

6

81.42 [70.19–84.48]

57.59 [50.91–60.12]

 < 2.2 × 10^–16

7

80.51 [70.61–84.65]

57.72 [49.58–61.42]

 < 2.2 × 10^–16

8

85.09 [77.12–90.93]

60.87 [51.36–70.79]

 < 2.2 × 10^–16

9

86.54 [77.32–92.26]

61.80 [52.44–72.56]

 < 2.2 × 10^–16