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Table 7 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 from low density panels to the 777K SNP panel 1,2,3

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

Concordance rate

Allelic R 2

Source

Mean

Scheffé test 4

Source

Mean

Scheffé test 4

Algorithm 5 (P-value < 0.0001)

Algorithm 5 (P-value < 0.0001)

FImpute

1.291

a

FImpute

1.203

a

Beagle

1.244

b

Beagle

1.145

b

Panel 6 (P-value < 0.0001)

Panel 6 (P-value < 0.0001)

90tK

1.351

a

90tK

1.286

a

90iK

1.343

b

90iK

1.275

b

50K

1.295

c

50K

1.210

c

15K

1.273

d

15K

1.181

d

20K

1.247

e

20K

1.146

e

8K

1.245

e

8K

1.144

e

6K

1.239

e

6K

1.135

e

3K

1.150

f

3K

1.013

f

Scenario 7 (P-value 0.0258)

Scenario (P-value 0.0346)

NE-NP

1.269

a

NE-NP

1.175

a

NE-P

1.267

b

NE-P

1.172

b

Algorithm*panel (P-value =0.0052)

Algorithm*panel (P-value =0.0107)

FImpute - 90tK

1.370

a

FImpute - 90tK

1.309

a

FImpute - 90iK

1.364

a

FImpute - 90iK

1.301

a

Beagle - 90tK

1.331

b

Beagle - 90tK

1.262

b

FImpute - 50K

1.322

b

Beagle - 90iK

1.249

b

Beagle - 90iK

1.322

b

FImpute - 50K

1.244

b

FImpute - 15K

1.300

c

FImpute - 15K

1.215

c

FImpute - 20K

1.271

d

Beagle - 50K

1.176

d

FImpute - 8K

1.269

d

FImpute - 20K

1.176

d

Beagle - 50K

1.269

d

FImpute - 8K

1.174

d

FImpute - 6K

1.262

d

FImpute - 6K

1.165

d

Beagle - 15K

1.245

e

Beagle - 15K

1.146

e

Beagle - 20K

1.222

f

Beagle - 20K

1.115

f

Beagle - 8K

1.221

f

Beagle - 8K

1.114

f

Beagle - 6K

1.215

f

Beagle - 6K

1.106

f

FImpute - 3K

1.169

g

FImpute - 3K

1.039

g

Beagle - 3K

1.130

h

Beagle - 3K

0.988

h

  1. 1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
  2. 2Interaction effects between Algorithm*Scenario and Panel*Scenario were not statistically significant (P > 0.05);
  3. 33K, 6K, 8K, 15K and 20K are low-density panels were imputed in two steps (firstly they were imputed to the 50K and then to the 777K SNP panel);
  4. 4Different letters within a group means that there is a statistical difference between two means (P < 0.05);
  5. 5Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
  6. 63K, 6K, 8K, 15K, 20K, 50K, 90iK and 90tK 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

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