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Table 5 Prediction accuracy with Lasso, SVML and MAG when the sample size is reduced from 100 to 25 % of the original size

From: Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations

 

Breed

Reduction

TPA

TNR

TPR

LD

K

locK

SVML

Brown Swiss

1.00

0.992 (0.0081)

0.981 (0.0237)

0.998 (0.0047)

0.0469

0.4212

0.4981

 

Brown Swiss

0.75

0.984 (0.0440)

0.983 (0.0521)

0.986 (0.0516)

0.0584

0.4165

0.4987

 

Brown Swiss

0.50

0.920 (0.1745)

0.871 (0.2961)

0.981 (0.0285)

0.0626

0.4237

0.4894

 

Brown Swiss

0.25

0.880 (0.1562)

0.738 (0.3751)

0.977 (0.0653)

0.0690

0.4183

0.4992

 

Fleckvieh

1.00

0.996 (0.0025)

0.999 (0.0009)

0.928 (0.0525)

0.0226

0.3392

0.4082

 

Fleckvieh

0.75

0.995 (0.0034)

0.998 (0.0014)

0.909 (0.0857)

0.0228

0.3252

0.4081

 

Fleckvieh

0.50

0.991 (0.0062)

1.000 (0.0001)

0.814 (0.1239)

0.0234

0.3195

0.3952

 

Fleckvieh

0.25

0.974 (0.0256)

1.000 (0.0003)

0.377 (0.2126)

0.0241

0.3197

0.4078

Lasso

Brown Swiss

1.00

0.987 (0.0112)

0.966 (0.0292)

1.000 (0.0000)

0.0469

0.4212

0.4981

 

Brown Swiss

0.75

0.986 (0.0338)

0.972 (0.0640)

1.000 (0.0000)

0.0596

0.4176

0.4776

 

Brown Swiss

0.50

0.967 (0.0472)

0.913 (0.1405)

1.000 (0.0000)

0.0586

0.4078

0.4862

 

Brown Swiss

0.25

0.945 (0.1117)

0.891 (0.1329)

0.958 (0.1443)

0.0683

0.4526

0.5151

 

Fleckvieh

1.00

0.997 (0.0017)

1.000 (0.0000)

0.942 (0.0369)

0.0226

0.3392

0.4082

 

Fleckvieh

0.75

0.996 (0.0034)

1.000 (0.0000)

0.944 (0.0869)

0.0229

0.3235

0.4050

 

Fleckvieh

0.50

0.987 (0.0309)

0.988 (0.0329)

0.923 (0.1545)

0.0248

0.3000

0.3876

 

Fleckvieh

0.25

0.979 (0.0247)

0.989 (0.0002)

0.825 (0.2020)

0.0250

0.3106

0.3961

MAG

Brown Swiss

1.00

0.984 (0.0152)

0.982 (0.0163)

0.992 (0.0112)

0.0469

0.4212

0.4981

 

Brown Swiss

0.75

0.983 (0.0155)

0.976 (0.0327)

0.989 (0.0161)

0.0589

0.4178

0.4832

 

Brown Swiss

0.50

0.982 (0.0194)

0.973 (0.0393)

0.987 (0.0259)

0.0586

0.4222

0.4891

 

Brown Swiss

0.25

0.978 (0.0352)

0.955 (0.0776)

0.992 (0.0331)

0.0683

0.4446

0.5097

 

Fleckvieh

1.00

0.994 (0.0030)

0.998 (0.0021)

0.991 (0.0030)

0.0226

0.3392

0.4082

 

Fleckvieh

0.75

0.994 (0.0032)

0.998 (0.0024)

0.939 (0.0603)

0.0225

0.3271

0.4069

 

Fleckvieh

0.50

0.994 (0.0048)

0.997 (0.0031)

0.917 (0.0871)

0.0239

0.3095

0.3962

 

Fleckvieh

0.25

0.993 (0.0074)

0.997 (0.0042)

0.896 (0.1438)

0.0251

0.3102

0.3960

  1. LD average linkage disequilibrium estimated around the mutation, K average genome-wide genomic relationships, locK average genomic relationships estimated using only SNPs around the mutation
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BMC Genomics

ISSN: 1471-2164

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