Fig. 2.

How consensus alleles improve the interpretability of the reference. a To build a consensus genome, we replaced minor alleles within the current reference with their major alleles (allele frequency (AF) > 0.5) across all bi-allelic SNPs. b Cumulative distributions of variants in the consensus genome (red line) and the current reference (blue line). c Cumulative distributions of AFs for variants in 100 randomly chosen personal genomes, computed against a consensus genome. d Distribution of the number of homozygous single nucleotide variants (SNVs) in 2504 personal genomes, computed against the reference, against an all-human consensus, the mean of the super-population consensuses and the mean of the population consensuses. The consensus reference for each of the five super-populations leads to an additional reduction in the number of homozygous variants in the personal genomes for each super-population (dark red curve). Further breakdown into 26 representative populations does not dramatically reduce the number of homozygous variants (dashed red line). Super-populations are defined broadly as: AFR African, AMR admixed American, EAS East Asian, EUR European, SAS South Asian