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Table 5 Average (standard deviation) of Similarity Indices If for haplotypes inferred with PHASE and with the DP algorithm from genotypes of simulated populations M and Cross.

From: Haplotype inference in crossbred populations without pedigree information

MAF PHASE DP
  Pop. M Cross pop. Pop. M Cross pop.
0.01 1.00 (0.01) 0.00 (0.00) 1.00 (0.01) 1.00 (0.01)
0.25 0.93 (0.04) 0.12 (0.28) 0.93 (0.04) 0.92 (0.04)
0.40 0.86 (0.05) 0.42 (0.30) 0.88 (0.03) 0.87 (0.05)
0.49 0.90 (0.03) 0.55 (0.25) 0.90 (0.03) 0.89 (0.03)
  1. Minor Allele Frequency in the base populations (MAF) was simulated between 0.01 and 0.49, 10 replicates were simulated for each MAF. Genotypes of simulated population F were included in the analyses with the DP algorithm. Parameter α was set equal to 1 in the analyses with DP.