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Table 1 Average imputation accuracy from the bovine 777 K SNP chip to whole-genome sequence on chromosome 1 and 29

From: Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy

 

Chromosome 1

Chromosome 29

 

HOL20

MIX80

HOL80

MIX140

HOL20

MIX80

HOL80

MIX140

Sequence (n)

1,912,451

1,912,451

1,91,2451

1,912,451

670,773

670,773

670,773

670,773

777 K chip (n)

41,868

41,868

41,868

41,868

13,556

13,556

13,556

13,556

No variation in reference set (n)1

1,178,683

710,480

894,633

616,808

385,137

221,137

283,516

187,904

No variation observed in validation set (n)1

-2

468,203

284,050

561,875

-2

164,000

101,621

197,233

No variation imputed in validation set (n)1

19,484

1,005

1,077

649

19,284

4,139

4,267

3,681

Obtained overall imputation accuracy (n)

672,416

690,895

690,823

691,251

252,796

267,941

267,813

268,399

average overall imputation accuracy (r)

0.70

0.83

0.88

0.89

0.59

0.74

0.80

0.82

standard deviation of r

0.32

0.27

0.25

0.24

0.37

0.32

0.29

0.28

  1. 1No variation was present in the genotype dosages of at least one of the 5 corresponding cross-validation sets, therefore the imputation accuracy (correlation) could not be computed.
  2. 2In scenario HOL20 the reference sets were the same as the validation sets, therefore all variants without variation in at least one cross-validation reference set are the same as the variants without variation in observed genotypes of the validation sets.