Figure 3

Exploring the effects of different sets of mapping parameters on BWA performance and runtime. Helicos sequencing reads recovered from the sample showing a finite radiocarbon date (13,389 ± 52BP) 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. Performance and runtime are estimated with reference to the standard default parameters.