Fig. 3

An example of Yin, Yang, and Mosaic haplotypes and a Denisovan diplotype from the segment 102 of chromosome 1. The alleles that match the human reference genome are shown as “0”, while the alternative alleles as “1”. The ancestral alleles are shown in black, and the derived ones are shown in red. Blue and yellow highlights demonstrate pieces of Yin (blue) and Yang (yellow) segments from which the Mosaic haplotype can be reconstructed. This Mosaic haplotype is constructed from 14 pieces and has 12 derived alleles. Ten Mosaic derived alleles (83%) match the Yin haplotype and only two Mosaic derived alleles match the Yang haplotype. The Denisovan diplotype is shown in the last row. For the diplotype “0” means that both parental alleles match the human reference genome, “2” means that both alleles match alternative alleles, “1” means that this ancestral Denisovan person is heterozygous at this particular allele, and “x” means that this allele is unresolved. The heterozygous status for our frequent GVs (MAF > 25%) is very rare for the Denisovan sequenced individual, so his homozygous diplotypes can be converted to haplotypes by the substitution of “2”s for “1”s