The overall quality of the Zlatý kůň genome — in terms of coverage depth and fraction of the genome covered — was high enough to support the analyses that Prüfer and colleagues published in 2021, and to provide confident assessments of ancestry, Neanderthal segment lengths, and pigmentation alleles.

The Neanderthal segment length analysis specifically required confident calling of the segments — identifying, across the genome, which stretches of sequence were of Neanderthal origin versus modern human origin.

This is done by comparing the ancient sequence to both modern human genomes and sequenced Neanderthal genomes, and identifying regions where the ancient individual shares variants specifically with Neanderthals rather than with modern humans.

The statistical analysis required to distinguish genuine Neanderthal-derived segments from noise and from regions of deep shared ancestry between humans and Neanderthals is sophisticated, and the confidence in the result depends on both the coverage of the ancient genome and the quality of the reference Neanderthal genomes.