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Table 2 Haplotypes and their frequencies for simulations and validation. When simulating under a non-null genetic model, the high-risk allele lies exclusively on the second haplotype. For validation purposes, haplotype frequencies are compared between software in samples of 1000 affected sib-pair families, averaged over 25 runs, under a non-null genetic model.

From: SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values

Marker haplotype Population frequency Estimated frequency of haplotype in LD with trait locus
   SLINK/SUP SIMLA
1-1-1-1-1-1 0.5 0.463 0.461
1-1-1-1-1-2 0.25 0.305 0.308
1-1-1-1-2-2 0.125 0.115 0.116
1-1-1-2-2-2 0.0625 0.0592 0.0578
1-1-2-2-2-2 0.0312 0.0293 0.0292
1-2-2-2-2-2 0.0156 0.0143 0.0143
2-1-1-1-1-1 0.0078 0.00764 0.00716
2-2-1-1-1-1 0.0040 0.00352 0.00376
2-2-2-1-1-1 0.0020 0.00188 0.00208
2-2-2-2-1-1 0.0010 0.00048 0.00060
2-2-2-2-2-1 0.0005 0.00016 0.00008
2-2-2-2-2-2 0.0004 0.00001 0.00004