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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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