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The number of SNP that failed to achieve ≥90% SNP call rate within each pure breed population (diagonal axis) and the proportion of these failed SNP in the breed represented by each column that were also in the breed represented by each row. All animals were predicted to be >87.5% pure. The number of purebred animals with in each population were 5,556 Angus, 779 Belgian Blue, 14,388 Charolais, 3,314 Hereford, 13,243 Holstein, 15,266 Limousin, 1,235 Shorthorn, and 3,469 Simmental

 
Angus Belgian Blue Charolais Hereford Holstein Limousin Shorthorn Simmental
Angus 63 0.862 0.892 0.843 0.803 0.892 0.813 0.823
Belgian Blue 0.784 57 0.872 0.735 0.774 0.852 0.784 0.823
Charolais 0.754 0.813 53 0.735 0.735 0.892 0.725 0.794
Hereford 0.843 0.813 0.872 63 0.735 0.852 0.754 0.774
Holstein 0.813 0.862 0.892 0.754 64 0.852 0.725 0.774
Limousin 0.784 0.823 0.921 0.754 0.735 55 0.725 0.794
Shorthorn 0.833 0.882 0.872 0.764 0.725 0.843 64 0.852
Simmental 0.813 0.892 0.921 0.764 0.754 0.892 0.835 62
1≥90 SNP.
285 to <90 SNP.
380 to <85 SNP.
475 to <80 SNP.
575 to <80 SNP.



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Mean genotype and allele concordance rates (CR) per animal before and after imputation between low– and high–call rate animal genotypes for each call rate category. The minimum and maximum individual animal concordance rates are in parenthesis

 
Before imputation
After imputation
After imputation
Call rate class Number of animals Genotype CR Allele CR Genotype CR noncalled SNP Allele CR noncalled SNP Genotype CR all SNP Allele CR all SNP
<40 49 0.393 (0.313, 0.573) 0.630 (0.537, 0.770) 0.406 (0.371, 0.463) 0.642 (0.602, 0.686) 0.402 (0.358, 0.486) 0.638 (0.585, 0.708)
40 to <50 63 0.481 (0.301, 0.761) 0.691 (0.532, 0.878) 0.433 (0.375, 0.545) 0.664 (0.604, 0.750) 0.456 (0.341, 0.634) 0.677 (0.579, 0.802)
50 to <60 84 0.606 (0.311, 0.899) 0.780 (0.526, 0.949) 0.487 (0.372, 0.764) 0.707 (0.595, 0.879) 0.553 (0.341, 0.846) 0.747 (0.561, 0.922)
60 to <70 59 0.768 (0.365, 0.980) 0.877 (0.593, 0.989) 0.601 (0.385, 0.890) 0.782 (0.605, 0.944) 0.710 (0.370, 0.953) 0.844 (0.595, 0.975)
70 to <75 48 0.860 (0.490, 0.977) 0.929 (0.727, 0.988) 0.698 (0.407, 0.910) 0.838 (0.686, 0.955) 0.815 (0.485, 0.952) 0.904 (0.718, 0.976)
75 to <80 48 0.898 (0.566, 0.933) 0.949 (0.779, 0.996) 0.728 (0.052, 0.945) 0.851 (0.382, 0.970) 0.859 (0.445, 0.983) 0.926 (0.686, 0.990
80 to <85 47 0.962 (0.640, 1.000) 0.981 (0.819, 0.999) 0.880 (0.121, 0.987) 0.936 (0.535, 0.985) 0.948 (0.547, 0.994) 0.973 (0.762, 0.996)
85 to <90 80 0.987 (0.957, 1.00) 0.993 (0.978, 0.999) 0.939 (0.851, 0.987) 0.967 (0.918, 0.993) 0.981 (0.947, 0.998) 0.990 (0.973, 0.999)
90 to <95 6 0.986 (0.982, 0.991) 0.993 (0.991, 0.996) 0.941 (0.927, 0.957) 0.969 (0.961, 0.978) 0.982 (0.997, 0.988) 0.991 (0.988, 0.994)
95 to <99 3 0.998 (0.998, 0.999) 0.999 (0.998, 0.999) 0.948 (0.916, 0.969) 0.973 (0.958, 0.981) 0.997 (0.996, 0.999) 0.999 (0.998, 0.999)



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The number and percentage of parentage errors on all high–call rate genotypes

 
Relationship Number of relationships Parentage errors (%)
Sire incorrect 44,491 13.28
Dam incorrect 13,529 10.18
Both sire and dam incorrect 5,424 3.13



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The mean, SD, minimum, and maximum percentage of SNP Mendelian inconsistencies detected between a parent–progeny pair per animal call rate category

 
Call rate category Number of animals Mean SD Minimum Maximum
<40 29 27.23 6.63 12.35 39.80
40 to <50 24 19.25 11.91 3.67 40.74
50 to <60 28 10.37 9.76 1.07 43.03
60 to <70 44 4.68 6.75 0.07 28.09
70 to <75 34 0.80 1.10 0.00 4.24
75 to <80 32 0.91 1.52 0.00 6.29
80 to <85 36 0.25 0.31 0.00 1.23
85 to <90 82 0.12 0.10 0.00 0.53
90 to <95 4 0.02 0.03 0.00 0.04
95 to <99 0