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Table 1 Extent of linkage disequilibrium and distance between two adjacent SNPs and correlations for elements of G matrices

From: Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle

No. of SNPs selected r 2 d(Mb) Correlation*
Mean SD Mean SD r D r N r A
100 0.008 0.011 25.98 3.15 0.61 0.51 0.59
200 0.017 0.027 12.86 1.95 0.74 0.64 0.72
500 0.032 0.060 5.10 1.03 0.82 0.79 0.86
1,000 0.048 0.077 2.55 0.62 0.89 0.88 0.92
2,000 0.057 0.093 1.27 0.39 0.94 0.94 0.96
4,000 0.066 0.108 0.65 0.65 0.97 0.97 0.98
6,000 0.077 0.121 0.44 1.03 0.98 0.98 0.99
8,000 0.086 0.136 0.33 0.66 0.99 0.99 0.99
10,000 0.096 0.151 0.26 0.45 0.99 0.99 0.99
20,000 0.144 0.215 0.13 0.29 0.99 0.99 0.99
30,000 0.187 0.261 0.09 0.24 0.99 0.99 0.99
38,502 0.204 0.275 0.07 0.20 - - -
  1. *Correlations between the diagonal (r D ), upper triangular (r N ) and all the elements (r A ) of two G matrices constructed using a given SNP subset and all available SNPs.
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BMC Genomic Data

ISSN: 2730-6844

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