Marking optical or PCR duplicates with picard vs. samtools flagstat
There are duplicates, in this line:

1636809 + 0 duplicates, gives 1636809/26595942 = 0.06154356

According to samtools documentation for flagstat:


  Provides counts for each of 13 categories based primarily on bit flags
  in the FLAG field. Each category in the output is broken down into QC
  pass and QC fail. In the default output format, these are presented as
  "#PASS + #FAIL" followed by a description of the category.


So you can usually take whatever is in the first column