For a given sample I have the 2,636,688 in the mapping_stats file for the number of UniqueFWDandREV which equals the number of UniqueFWDorREV. However if I run the ngsutils command bamutils filter -mapped -eq NH:i 1 on the corresponding bam file, the reported number of retained alignments is so 5273384, thus 2636692 unique aligners (this is paired end).
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