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Table 1 Comparison of linkage analysis results between microsatellite and SNP based genome scans

From: Resampling methods to reduce the selection bias in genetic effect estimation in genome-wide scans

    Location estimates (mode) Power to detect linkage Mean test statistic
Pop Chr. True location (cM) MS (cM) SNP (cM) MS SNP MS SNP
AI 1 168.98 169.85 167.4 4/100 7/100 4.33 4.56
  3 299.32 293.61 295.6 22/100 a 24/100 4.79 4.77
  5 5.45 7.34 5.94 11/100 11/100 4.53 4.63
  9 5.88 4.78 5.54 10/100 9/100 4.39 4.38
KA 1 168.98 169.97 168.0 2/100 2/100 4.07 4.24
  3 299.32 293.75 295.9 14/100 17/100 4.41 4.77
  5 5.45 7.01 5.69 20/100 40/100 4.67 4.71
  9 5.88 6.80 5.96 52/100 45/100 4.95 4.92
DA 1 168.98 169.95 168.8 82/100 89/100 5.20 5.43
  3 299.32 293.62 295.7 48/100 56/100 4.89 4.77
  1. a Bold text indicates the cases in which linkage was detected in replicate 1 with genome-wide significance using either the microsatellite or the SNP markers (as reported in Table 2).