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• Unique singleton 
  • fraction of alignments corresponding to the reads where only one of the paired reads can be uniquely aligned
• Unique paired 
  • fraction of alignments corresponding to the reads where both of the paired reads can be uniquely aligned
• Non-unique singleton
  • fraction of singletons that align to multiple locations
• Non-unique paired
  • fraction of paired reads that align to multiple locations

Note: for paired-end reads, if one end is aligned, the mate is not aligned, the alignment rate calculating will include the read as the numerator, also since the mate is not aligned, we will also include this read in the unaligned data node (if the generate unaligned reads data node option is selected) for 2nd stage alignment, this will generate discrepancy between total reads and "unaligned reads + total reads * alignment rate", because reads with only one mate aligned are counted twice  .

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