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Table 1 Genomic coverage of genotype panels of SNP chip only and combined approach

From: A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

MAF bin

Estimated r 2 ≥ 0.8

Estimated r 2 ≥ 0.4

Exome chip

SNP chip

Combined

Exome chip

SNP chip

Combined

ALL

0.367

0.435

0.560

0.492

0.749

0.818

≥5 %

0.600

0.794

0.901

0.756

0.953

0.983

1–5 %

0.374

0.403

0.588

0.510

0.799

0.881

0.5–1 %

0.192

0.146

0.290

0.290

0.585

0.686

<0.5 %

0.107

0.079

0.172

0.192

0.491

0.591

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BMC Genomics

ISSN: 1471-2164

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