Exploring the effects of different sets of mapping parameters on BWA performance and runtime. Sequencing reads recovered from the sample showing infinite radiocarbon date were aligned using different combinations of mapping parameters using the BWA aligner. Reads were considered of high-quality when mapping uniquely to the EquCab2 genome but not against the human genome (assembly hg19) and showing mapping qualities of at least 25. For Illumina, positive hits were filtered for PCR duplicates (see Methods). Performance and runtime are estimated with reference to the standard default parameters. Left: Helicos tSMS reads. Right: Illumina reads.