Sequencing Mitogenome Control Region of Horses

The sequences of the 246 bp mitogenome control region fragment for modern horses were obtained using Sequencing Analysis Software v7.0 (primary analysis tool, Thermo Fisher Scientific) and Sequence Scanner Software v2.0 (viewer, Thermo Fisher Scientific).
For ancient and medieval horses, the sequences of the 246 bp mitogenome control region fragment were obtained using PALEOMIX BAM Pipeline v1.3.2 [28 (link)]. Removal of adapter sequences and collapse of reads was performed using AdapterRemoval v2.2.2 [29 (link)]. Sequence aligner bwa v0.7.15 [30 (link)] was used to perform collapsed read alignment against the reference sequence of the horse mitogenome (GenBank accession №: NC_001640.1), with a minimum read mapping quality of 25. The MapDamage v2.2.0 computational framework [31 (link)] helped recalculate base quality scores according to the probability of post-mortem DNA damage at each position in the sequence. The bioinformatics software platform Geneious Prime v2020.2.4 (https://www.geneious.com; Biomatters Ltd., Auckland, New Zealand) was used to visualize the resulting alignment and obtain a consensus sequence of the studied fragment of the mitogenome control region in which the quality of each base would be higher than 60% of the total adjusted base quality.