Fraction of paired alignments in the BAM file where 2 alignments total share the same start position:
StartPosition.DupLevel1Rate= # of start and end position pairs with 2 alignments / Alignment_Mapped
Alignments with same mapping position (start and end position of a read pair) are considered as duplicates.
These metrics are only for paired-end reads. For single-end reads, please use Duplication_StartPosition.DupLevel2Rate.