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Table 3 Imputation accuracies compared to true genotypes in the GBS loci (GBSr) and reliabilities of genomic prediction using GBS data imputed by FImpute with or without pedigree information (GcFIped or GcFI) at depth = 4 and MAF ≥ 0.01, averaged over 10 replicates. The imputation was performed after genotype correction (i.e., GcFIped and GcFI). Note: Depth = 4 (1) or Depth = 4 (1 & 2) indicated the genotypes with read = 1 or 1 and 2 were set as missing genotypes. Standard errors were shown within bracket

From: Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations

 Depth = 4Depth = 4Depth = 4 (1)Depth = 4 (1 & 2)
 FIFIpedGcFIGcFIpedGcFIGcFIpedGcFIGcFIped
Correct genotype rate0.905 (<  0.0005)0.920 (<  0.0005)0.915 (<  0.0005)0.919 (<  0.0005)0.927 (<  0.0005)0.935 (<  0.0005)0.942 (<  0.0005)0.950 (<  0.0005)
Correlation0.946 (<  0.0005)0.955 (<  0.0005)0.951 (<  0.0005)0.954 (<  0.0005)0.960 (<  0.0005)0.965 (<  0.0005)0.971 (<  0.0005)0.976 (<  0.0005)
Prediction reliability0.666 (0.0253)0.670 (0.0245)0.666 (0.0248)0.668 (0.0245)0.674 (0.0246)0.679 (0.0246)0.683 (0.0242)0.689 (0.0246)