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

Fingerprint panel index	Genotype consistency rate (%)		P-value
	Matched pairs (N = 240)	Mismatched pairs (28,680 permutations)
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

The index of fingerprint panels was identical to that in Table 1. The genotype consistency rate ranges, displayed in the format of [minimum–maximum], were presented in brackets. P-value showed the significance of one-sided t-tests