Sambamba_flagstat outputs statistics drawn from read flags.

The first line contains numbers of QC-passed and QC-failed reads. Then come pairs of numbers, the former for QC-passed reads, the latter for QC-failed ones:

• duplicates
• mapped reads (plus percentage relative to the numbers from the first line)
• reads with 'is_paired' flag set
• paired reads which are first mates
• paired reads which are second mates
• paired reads with 'proper_pair' flag set (plus percentage relative to the numbers of QC-passed/failed reads with 'is_paired' flag set)
• paired reads where both mates are mapped
• paired reads where read itself is unmapped but mate is mapped
• paired reads where mate is mapped to a different chromosome
• the same as previous but mapping quality is not less than 5