Table 1 Sequence error estimation

Heterozygous in NGS data

891,514

815,810

833,149

832,549

812,952

Heterozygous in BeadChip data

16,426

15,469

15,873

15,987

14,008

Homozygous in BeadChip data

33,403

34,360

33,956

33,842

35,821

Heterozygous in NGS and BeadChip data

3,555 (7.14 %)

3,239 (6.50 %)

3,306 (6.64 %)

3,396 (6.82 %)

2,960 (5.94 %)

Heterozygous in BeadChip and homozygous in NGS data

12,867 (25.83 %)

12,223 (24.54 %)

12,565 (25.22 %)

12,589 (25.27 %)

11,047 (22.17 %)

(False-negative rate)

Homozygous in BeadChip and heterozygous in NGS data

19 (3.8 × 10⁻⁴of all 49,813 positions validated in BeadChip)

29 (5.8 × 10⁻⁴of all 49,813 positions validated in BeadChip)

38 (7.6 × 10⁻⁴of all 49,815 positions validated in BeadChip)

49 (9.8 × 10⁻⁴of all 49,823 positions validated in BeadChip)

28 (5.6 × 10⁻⁴of all 49,824 positions validated in BeadChip)

(False-positive rate)

Homozygous in >10 Mb BeadChip ROH regions and heterozygous in NGS data

5.9 × 10⁻⁵

3.8 × 10⁻⁵

2.2 × 10⁻⁵

3.1 × 10⁻⁴

2.6 × 10⁻⁵

(Robust false-positive rate)