These tracks show probability of introgression obtained by ARGweaver using a population-based model. Methods are described in Hubisz,Williams,Siepel(2019). These results are the main ones discussed in the paper, using a migration time of 250kya and a super-archaic divergence time of 1Mya.
The "Regions" track shows the predicted introgressed regions using a posterior probability cutoff of 0.5. There is one sub-track per individual, with the source of introgression indicated by the colors. (Neanderthal=red, Denisovan=blue, Human=green, Super-Archaic hominin=gray). Darker shades are used to indicate homozygous introgressed regions.
The "Variants" track shows the locations of variants for the individuals used in this analysis. The variants were phased using ARGweaver, and the phase for the final sampled ARG is displayed. Only sites that are variant within the hominid samples are shown; the colored sites are the ones that do not match chimp. At sites where chimp is not available, the colored sites are the ones that share the minior allele. Masked sites are not indicated in this track, though all colored sites are not masked. The colors alternate at each adjacent variant site, in order to make it clear visually whether sites that appear to align vertically are from the same position.
The remaining tracks show the posterior probability of each type of introgression event in each individual, averaging across MCMC iterations.