Supplementary Figure 2: The accuracy of imputing sequence variant genotypes assessed in Montebeliarde, Normande and Danish Red cattle using 1000 Bull Genomes Run4. | Nature Genetics

Supplementary Figure 2: The accuracy of imputing sequence variant genotypes assessed in Montebeliarde, Normande and Danish Red cattle using 1000 Bull Genomes Run4.

From: Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Supplementary Figure 2

a, Accuracy was assessed for sequence variants on chromosomes 1, 20 and 25 using FImpute. The accuracy of imputing genotypes was calculated by masking the sequence genotypes of 14 randomly selected animals per breed from 1000 Bull Genomes Run4 to those on the Illumina BovineHD BeadChip and then imputing all sequence variants using FImpute45 with all other sequences (n = 1,133) as a reference. The squared correlation (r2) between the real sequence variant called genotypes and the imputed variant genotypes was taken as the accuracy of imputation. The accuracy of imputing sequence variant genotypes is plotted by minor allele frequency. b, The accuracy of imputation to sequence variants in Holstein and Jersey cattle was compared for FImpute and Beagle. The accuracy was assessed for sequence variants on chromosome 14. The accuracy of imputing genotypes was calculated by masking the sequence genotypes of 25 randomly selected animals per breed from 1000 Bull Genomes Run4 to those on the Illumina BovineHD BeadChip and then imputing all sequence variants using FImpute and Beagle with all other sequences (n = 1,122) as a reference.

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