Skip to main content

Table 1 Genotype imputation performance with different filtering criteria

From: Ultra-low-coverage genome-wide association study—insights into gestational age using 17,844 embryo samples with preimplantation genetic testing

Filtering criteria

SNP number

Genotype accuracy

Allele accuracy

None

167,814

0.584

0.758

Known SNP in 1000G reference panel

141,161

0.578

0.751

INFO score ≥ 0.1

156,835

0.591

0.771

INFO score ≥ 0.2

126,331

0.618

0.794

INFO score ≥ 0.3

84,932

0.656

0.815

INFO score ≥ 0.4

48,176

0.7

0.834

MAF ≥ 0.05

162,788

0.597

0.777

HWE p-value > 1e−9

84,237

0.595

0.695

HWE p-value > 1e−6

77,419

0.596

0.692

HWE p-value > 1e−3

65,561

0.599

0.687

HWE p-value > 1e−6 and INFO score ≥ 0.1

68,505

0.610

0.713

HWE p-value > 1e−6 and INFO score ≥ 0.2

55,972

0.646

0.751

HWE p-value > 1e−6 and INFO score ≥ 0.3

42,202

0.681

0.786

HWE p-value > 1e−6 and INFO score ≥ 0.4

28,773

0.715

0.818

  1. Totally 16,000 samples with an average of 0.04× sequencing coverage were used for imputation