 
Hits
  
Runtime


Gap Extend Penalty

11

9.9%

10.2%

22.9%

22.7%

25.5%

Gap Extend Penalty

11

1.7x

1.5x

1.6x

1.6x

1.6x

9

9.9%

10.2%

22.9%

22.7%

25.5%

9

1.8x

1.6x

1.6x

1.6x

1.6x

7

9.9%

10.2%

22.9%

22.7%

25.6%

7

1.7x

1.7x

1.6x

1.7x

1.7x

5

9.7%

10.0%

22.6%

22.5%

25.3%

5

1.6x

1.7x

1.7x

1.7x

1.7x

4

9.7%

9.9%

22.6%

22.5%

25.3%

4

1.6x

1.6x

1.8x

1.7x

1.6x

 
4

5

7

9

11
  
4

5

7

9

11

 
Gap Open Penalty
  
Gap Open Penalty

 Sequencing reads recovered from the sample showing infinite radiocarbon date were aligned using different combinations of penalties for opening (−O) and extending (−E) gaps using the BWA aligner with seed disabled (−l 1024) and allowing a maximum number of two indels (−o 2) possibly located at read ends (−i 0). Shifts in the percentage of highquality hits recovered and total runtime are reported relative to the values observed using BWA default parameters, with the result for default gap penalties shown in green. Reads were considered of highquality when mapping uniquely to the EquCab2 genome but not against the human genome (assembly hg19) and showing mapping qualities of at least 25.