Open Access Research article

Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle

Mehar S Khatkar13*, Gerhard Moser13, Ben J Hayes23 and Herman W Raadsma13

Author Affiliations

1 Reprogen - Animal Bioscience, Faculty of Veterinary Science, University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia

2 Department of Primary Industries, Biosciences Research Division, Bundoora, Victoria, 3083, Australia

3 Dairy Futures Cooperative Research Centre (CRC), Bundoora, Victoria, Australia

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BMC Genomics 2012, 13:538  doi:10.1186/1471-2164-13-538

Published: 8 October 2012

Additional files

Additional file 1:

Figure S1. Distribution of pedigree kinship among animals within different datasets shown as boxplots.

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Additional file 2:

Accuracy of imputation of genotypes (%) and mean allelic error rate (%) up to 50K using three imputation methods. This file presents the results from different scenarios of imputation up to 50K. These scenarios were generated by using different proportion of animals in reference and test sets for varying SNP density (3K, 5K, 10K, 20K and 35K evenly spaced and Illumina Bovine3K) in the test set. The scenarios 1–6 used 1363 (50%) bulls, scenarios 7–12 used 681 (25%) bulls, scenarios 13–18 used 272 (10%) bulls, scenarios 19–24 used 136 (5%) bulls and scenarios 25–30 used 27 (1%) bulls in the reference set and the rest of animals in the test set. The scenarios 31–36 used all the bulls in the reference and all the cows in the test set. The scenarios 37–42 used all the cows in the reference and all the bulls in the test set. The results shown are for chromosome 20.

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Additional file 3:

Effect of pedigree kinship between test and reference animals on the mean allelic error rate (%) of imputation. This file presents the results of association of kinship with error rate of imputation in the form of bar charts from 42 scenarios of imputation up to 50K as given in Additional file 2. On Y-axis, is highest kinship estimate of a test animal with any of the reference animals and is presented as four interval categories viz. 0.0-0.01, 0.01-0.1, 0.1-0.2 and 0.2-0.4. On X-axis is the mean allelic error rate (%) on imputation.

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