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Table 6 Means and ranges of generalized measures of squared correlations for digenic (gametic and composite), trigenic, quadrigenic and zygotic disequilibria averaged over all syntenic (intra-chromosome) SNP pairs and over all non-syntenic (inter-chromosome) SNP pairs across the composite beef genome

From: Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle

LD Intra-chromosome   Inter-chromosome
# of pairs Strength   Power*   # of pairs Strength Power*
Mean Range   Mean Range   Mean Range Mean Range
φ D AB 2 r D AB 2 a 36131611 0.0105 0.0082-0.0126   0.4946 0.4432-0.5385   83686490 0.0044 0.0041-0.0047 0.3526 0.3338-0.3740
φ Δ AB 2 a 36131636 0.0097 0.0077-0.0117   0.4945 0.4449-0.5400   893686490 0.0044 0.0041-0.0047 0.3526 0.3338-0.3740
φ D ABB 2 a 11158132 0.0035 0.0028-0.0045   0.1264 0.1043-0.1459   272879855 0.0033 0.0027-0.0042 0.1198 0.1025-0.1404
φ D AAB 2 a 11224541 0.0034 0.0030-0.0041   0.1257 0.1098-0.1450   273790442 0.0034 0.0027-0.0042 0.1222 0.1030-0.1428
φ Δ AABB 2 a 36128429 0.0013 0.0012-0.0016   0.0740 0.0643-0.0921   893685393 0.0010 0.0010-0.0011 0.0540 0.0513-0.0579
φ ω AB 2 r ω AB 2 a 36071428 0.0029 0.0025-0.0034   0.1726 0.1577-0.1887   893012960 0.0016 0.0015-0.0016 0.1145 0.0105-0.1205
  1. * Proportion of SNP pairs that X2 exceeded 3.84, the 5% critical value of χ ( 1 ) 2 .
  2. a The generalized measures of squared correlation for digenic, trigenic and quadrigenic disequilibria: φ D AB 2 = X D AB 2 / n , φ Δ AB 2 = X Δ AB 2 / n , φ D ABB 2 = X D ABB 2 / n , φ D AAB 2 = X D ABB 2 / n , φ Δ AABB 2 = X Δ AABB 2 / n a n d φ ω AB 2 = X ω AB 2 / n , where n is the number of animals at individual SNP pairs. The Generalized measures of gametic and zygotic LD ( φ GLD 2 and φ ZLD 2 ) are based on an exact 2 × 2 contingency table and thus they are simply the squared correlations, i.e., φ GLD 2 = r GLD 2 and φ ZLD 2 = r ZLD 2 .