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Table 8 Analysis of variance performed on the average concordance rate and allelic R 2 of the animals in the imputation population from each scenario for imputation to the 777K SNP panel by one or two steps 1,2

From: Accuracy of genome-wide imputation in Braford and Hereford beef cattle

Concordance rate

Allelic R 2

Source

Mean

Scheffé test 3

Source

Mean

Scheffé test 3

Step 4 (P-value < 0.0001)

Step 4 (P-value < 0.0001)

Two-step

1.231

a

Two-step

1.125

a

One-step

1.110

b

One-step

0.997

b

Algorithm 5 (P-value < 0.0001)

Algorithm 4 (P-valeu 0.0001)

FImpute

1.202

a

FImpute

1.080

a

Beagle

1.140

b

Beagle

0.997

b

Panel 6 (P-value < 0.0001)

Panel 6 (P-value < 0.0001)

15K

1.236

a

15K

1.130

a

20K

1.229

b

20K

1.120

a

8K

1.180

c

8K

1.052

b

6K

1.167

d

6K

1.034

c

3K

1.042

e

3K

0.855

d

Scenario 7 (P-value 0.7638)

Scenario 7 (P-value 0.9983)

NE-NP

1.171

a

NE-NP

1.038

a

NE-P

1.170

a

NE-P

1.038

a

Step*Algorithm (P-value < 0.0001)

Step*Algorithm (P-value < 0.0001)

Two-step - FImpute

1.254

a

Two-step - FImpute

1.154

a

Two-step - Beagle

1.208

b

Two-step - Beagle

1.095

b

One-step - FImpute

1.149

c

One-step - FImpute

1.006

c

One-step - Beagle

1.072

d

One-step - Beagle

0.898

d

Step*Panel (P-value < 0.0001)

Step*Panel (P-value < 0.0001)

Two-step - 15K

1.274

a

Two-step - 15K

1.183

a

Two-step - 20K

1.247

b

Two-step - 20K

1.147

b

Two-step - 8K

1.246

b

Two-step - 8K

1.145

b

Two-step - 6K

1.239

b

Two-step - 6K

1.136

b

One-step - 20K

1.210

c

One-step - 20K

1.094

c

One-step - 15K

1.198

c

One-step - 15K

1.078

c

Two-step - 3K

1.149

d

Two-step - 3K

1.013

d

One-step - 8K

1.114

e

One-step - 8K

0.960

e

One-step - 6K

1.094

f

One-step - 6K

0.932

e

One-step - 3K

0.936

g

One-step - 3K

0.696

f

  1. 1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
  2. 2Interaction effects between step*scenario, algorithm*panel, algorithm*scenario and panel*scenario were not statistically significant (P > 0.05);
  3. 3Different letters within a group means that there is a statistical difference between two means (P < 0.05);
  4. 4One-step is the imputation from the low-density panels to the 777K SNP panel and two-step is the imputation from low-density panels to 50K SNP panel and after the imputation from 50K SNP panel to 777K SNP panel;
  5. 5Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
  6. 63K, 6K, 8K, 15K, and 20K are low-density panels;
  7. 7Scenarios for imputation to the 777K SNP panel. (NE-P) - using Nellore genotypes in the reference population and considering pedigree information; (NE-NP) - using Nellore genotypes in the reference population and not using pedigree information.
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BMC Genomic Data

ISSN: 2730-6844

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