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Table 2 NPL statistics in the presence and absence of LD

From: Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium

  Simulated   Founders genotyped Founders ungenotyped
Chromosome Gene LD LD reduction Mean NPLall ± SD (Range) Mean KC-LOD ± SD (Range) Mean NPLall ± SD (Range) Mean KC-LOD ± SD (Range)
2 No Yes Not Reduced 0.01 ± 0.93 (-2.28, 2.96) 0.01 ± 0.33 (-1.17, 1.72) 0.51 ± 0.91 (-1.57, 3.15) 0.19 ± 0.38 (-0.68, 2.02)
    Reduced 0.00 ± 0.92 (-2.29, 2.86) 0.00 ± 0.33 (-1.24, 1.64) 0.36 ± 0.90 (-1.82, 2.79) 0.14 ± 0.35 (-0.77, 1.60)
4 No No Not Reduced -0.01 ± 0.92 (-2.81, 2.26) -0.01 ± 0.30 (-1.32, 1.24) -0.02 ± 0.82 (-2.77, 2.21) 0.00 ± 0.28 (-1.35, 1.27)
    Reduced -0.03 ± 0.93 (-2.80, 2.23) -0.01 ± 0.31 (-1.32, 1.26) -0.04 ± 0.83 (-2.68, 2.18) -0.01 ± 0.29 (-1.31, 1.32)
3 Yes Yes Not Reduced 3.89 ± 1.03 (1.64, 6.69) 3.22 ± 1.64 (0.56, 9.18) 3.72 ± 0.98 (1.72, 6.46) 3.25 ± 1.61 (0.58, 8.68)
    Reduced 3.84 ± 1.04 (1.64, 6.73) 3.20 ± 1.68 (0.57, 9.44) 3.46 ± 1.00 (1.50, 6.24) 3.03 ± 1.62 (0.48, 8.31)
1 Yes No Not Reduced 4.61 ± 1.05 (2.15, 8.51) 4.06 ± 1.80 (0.88, 11.79) 3.79 ± 0.95 (1.73, 7.18) 3.22 ± 1.58 (0.70, 9.52)
    Reduced 4.58 ± 1.03 (2.13, 8.42) 4.05 ± 1.77 (0.87, 11.67) 3.71 ± 0.93 (1.32, 6.89) 3.19 ± 1.53 (0.42, 9.06)
  1. 100 replicates, allele frequencies from file, statistics calculated at five evenly spaced intervals between markers.