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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