Fig 1.
General process for creating the study sample for imputation.
The reference panel was masked to mimic a commercial SNP array, resulting in a study sample which contains the same individuals as the reference panel.
Table 1.
Calculating concordance (P0) and IQS from imputed genotype probabilities and actual genotypes.
The table was created by summing over probabilities for all N individuals (n = 1 to N) in each cell with pij_n representing the probability that the nth individual has the imputed genotype i and actual genotype j, where 1 corresponds to AA, 2 corresponds to AB, and 3 corresponds to BB. N1 = number of individuals with AA actual genotype, N2 = number of individuals with AB actual genotype, N3 = number of individuals with BB actual genotype, and N = number of total individuals.
Fig 2.
IQS, squared correlation, concordance rate, and BEAGLE R2 are shown in MAF bins.
Mean accuracy of SNPs in each MAF bin (defined by 0.01 increments with N = 13,442 variants total) is denoted by the red dots and the bars indicate one standard deviation (above and below the mean). These results are produced by using the 1000 Genomes AFR reference population as the study sample with Omni 2.5M typed coverage on chromosome 15.
Fig 3.
IQS, squared correlation, concordance rate, and BEAGLE R2 are shown in max r2LD bins.
Mean accuracy of SNPs in each MAF bin (defined by 0.01 increments with N = 13,442 variants total) is denoted by the red dots and the bars indicate one standard deviation (above and below the mean). These results were produced by using the 1000 Genomes AFR reference population as the study sample with Omni 2.5M typed coverage on chromosome 15.
Fig 4.
Scatterplots of squared correlation and IQS.
Data for all 13,442 variants are displayed in panel A, while the results for variants with MAF>5% (N = 6,480) are found in panel B. The line y = x is denoted in red.
Fig 5.
Scatterplots of IQS, squared correlation, and BEAGLE R2.
Panels A and B display all 13,442 variants, and panels C and D display variants with MAF>5% (N = 6,480). The line y = x is denoted in red.
Fig 6.
Scatterplots of IQS, squared correlation, and BEAGLE R2 using the cosmopolitan reference panel and the African American nicotine dependence study sample for chromosome 15.
Data for all 1,545 variants are displayed in panel A, B, and C while the results for variants with MAF>5% (N = 631) are found in panel D, E, and F. These results were generated using Omni SNP coverage. The line y = x is denoted in red.