Additional file 1: Figure S1. of Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome
Long distance LD pr. Mb separated by the chromosome for each population LD for each SNP pair with a distance between 10Â kb and 1Â Mb taken into account. Figure S2. Accuracy and yield of imputation between each location of SNPs. Figure S3. Comparing minor allele frequencies of SNPs between imputed and actual genotypes before quality control of imputed results separately plot by each SNP location. Figure S4. Comparing allele frequencies of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted by each SNP location. Figure S5. Proportion of SNPs with lower AF after imputation vs initial AF. Figure S6. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes before quality control of imputed results separately plotted by each SNP location. Figure S7. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted according to each SNP location. Figure S8. Average linkage disequilibrium as r-squared for each region. SNPs were assigned to gene locations. Figure S9. LD, measured as r2, plotted against physical distance. (PDF 1286Â kb
