Additionally, ancient DNA shows characteristic patterns of chemical damage — particularly the conversion of cytosine bases to uracil at the ends of fragments — that serve as a quality control check (genuine ancient DNA shows these damage patterns; contaminating modern DNA does not).

The prepared library was then sequenced using high-throughput sequencing technology, producing billions of short sequence reads.

These reads were aligned to a reference human genome to determine where in the genome each read originated.

The alignment is complicated by the short fragment lengths and the damage patterns, but sophisticated bioinformatics pipelines handle these challenges.

The resulting aligned reads provided coverage across the Zlatý kůň genome — though not uniform coverage.

Some regions were sequenced many times over, providing confident determination of the sequence at those positions; other regions were covered only once or twice, providing less certainty.