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Table 1 Exploring BWA performance and runtime with different combinations of penalties for opening and extending gaps on Helicos tSMS reads

From: Improving ancient DNA read mapping against modern reference genomes

   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
  1. 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 high-quality 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 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.