From Array Suite Wiki
Specifies the number of mappings (or alignments) where the read was marked as a PCR or optical duplicate.
This is calculated using the FLAG statistic from the BAM/SAM file. It applies to the Bit flag of 0x400 or 1024 as an integer when multiple reads (or fragments, for paired-end) are mapped to the same location, and share the same read sequence. Only the first read in this read group will NOT be mapped as a duplicate.
This uses the BAM duplicate FLAG to identify duplicates.
Aligned QC Reports
Duplicates in DNASeqQCMetricsTable and RNASeqQCMetricsTable are defined as alignments with the same start position and end position, or fragments with same range (start and end positions of read1 and read2 in a pair).