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Table 6 Per-variant mean and standard deviations for imputation quality statistic (IQS) for 850 K imputation in the TAUR dataset based on the starting assay density

From: A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle

Starting assay

Starting density

Mean IQS

SD IQS

Mean IQS (low MAF)a

SD IQS (low MAF)a

ULD

6394

0.9095

0.1766

0.7720

0.3503

GGP-LD

16,854

0.9612

0.1225

0.8969

0.2604

SNP50

44,366

0.9745

0.1154

0.9121

0.2468

GGP-90KT

70,581

0.9796

0.1104

0.9220

0.2402

GGP-HD

125,446

0.9832

0.1032

0.9319

0.2264

  1. aVariants with minor allele frequencies < 0.1
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Genetics Selection Evolution

ISSN: 1297-9686