Estimating Individual Admixture Proportions from Next Generation Sequencing Data

Supporting Information

Supporting Information

Supporting Information - File S1, Figures S1-S19, and Table S1 (PDF, 379 KB)
File S1 - EM algorithm (PDF, 139 KB)
Figure S1 - Average individual depth for 1000 genomes sequencing data (PDF, 34 KB)
Figure S2 - Maximum deviation of estimated admixture proportions from true admixture proportions (PDF, 48 KB)
Figure S3 - Scenario B (low depth 2X) with 50 samples for 100,000 SNP sites simulated from HapMap frequencies. (PDF, 37 KB)
Figure S4 - Scenario B (low depth 2X) with 50 samples for 100,000 SNP sites simulated from HDGP frequencies. (PDF, 37 KB)
Figure S5 - Scenario A (variable depths between 1X and 6X) with 50 samples for 100,000 SNP sites simulated from HapMap frequencies. (PDF, 38 KB)
Figure S6 - Scenario A (variable depths between 1X and 6X) with 50 samples for 100,000 SNP sites simulated from HDGP frequencies. (PDF, 38 KB)
Figure S7 - Scenario C simulations based on HapMap frequencies (PDF, 38 KB)
Figure S8 - Scenario C simulations based on HGDP frequencies (PDF, 38 KB)
Figure S9 - Scenario D simulations (variable depth bewteen 0.5X and 6X and varying range of admixture proportions). (PDF, 71 KB)
Figure S10 - Scenario D simulations (variable depth bewteen 0.5X and 6X and varying range of admixture proportions). (PDF, 67 KB)
Figure S11 - RMSD for 100 simulations of scenario D for each of the two sets of allele frequencies in the ancestral populations (PDF, 34 KB)
Figure S12 - Maximum deviance for 100 simulations of scenario D for each of the two sets of allele frequencies in the ancestral populations (PDF, 34 KB)
Figure S13 - Maximum deviance for all individuals in the 100 simulations of scenario D for the HGDP allele frequencies in the ancestral populations, stratified according to which of the 14 different admixture proportions we have simulated (shown in figure 12). (PDF, 37 KB)
Figure S14 - Maximum deviance for the low depth individuals in the 100 simulations of scenario D for the HGDP allele frequencies in the ancestral populations, stratified according to which of the 14 different admixture proportions we have simulated, and have a sequencing depth smaller than 1.5 (shown in figure 12). (PDF, 37 KB)
Figure S15 - Maximum deviance for the high depth individuals in the 100 simulations of scenario D for the HGDP allele frequencies in the ancestral populations, stratified according to which of the 14 different admixture proportions we have simulated, and having a sequencing depth higher than 5 (shown in figure 12). (PDF, 37 KB)
Figure S16 - Estimated admixture proportions from both SNP chip (top) and low depth sequencing data from the 1000 genomes. (PDF, 44 KB)
Figure S17 - Estimated admixture proportions from both SNP chip (top) and low depth sequencing data from the 1000 genomes. (PDF, 47 KB)
Figure S18 - Estimated admixture proportions from both SNP chip and low depth sequencing data from the 1000 genomes (PDF, 38 KB)
Figure S19 - Admixture using two different genotype likelihood estimators (PDF, 39 KB)
Table S1 - Table showing the fraction of times the EM algorithm has converged to the same maximum (PDF, 59 KB)