Fig. 2
The spectrum of genome-wide variant frequency and LD of Tibetans. A Comparison of SNV counts of MAF among the 1001 WGS data and the published data. The 1001 WGS data is much more powerful in detecting rare variants than the published data. B The distribution of HWE deviation for SNVs with large between-population divergences (FST(Tibetan-Han) > 0.1), and the cutoff of HWE deviation is 1e − 6. C Validation by Sanger sequencing of three HWE-deviated SNVs with high FST(Tibetan-Han). The top panel shows the electro-morph of Sanger sequencing of the three SNVs. The histograms in the middle indicate the minor allele frequencies (MAF) of the three SNVs from three datasets, including the WGS data of 1001 Tibetans (in blue), the 96 random samples from the 1001 WGS data (in green), and the Sanger sequencing data of 96 samples (in red). The p values under the histograms indicate the significance levels of HWE deviation of the three SNPs based on the three datasets. D Comparison of the LD decay patterns between Tibetans and other world populations. The dashed box indicates a distinctive LD decay pattern of Tibetans. For the decay of long genomic regions (> 100 kb), Tibetans show a slower decay (reflected by the higher r.2 values) than those of other world populations, an indication of extended haplotype homozygosity. E The correlation of DAF (derived allele frequency) of the genome-wide SNVs from the 1001 Tibetan WGS data and the 3008 Tibetan array data [8] imputed by 1KTGP. F The correlation map when imputed by 1KGP3