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

Fingerprint panel index	Genotype consistency rate (%)		P-value
	Matched pairs (N = 94)	Mismatched pairs (4371 permutations)
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

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