How does Li and Durbin's BWA paper compare alignment programs on real data? Li and Durbin's "Fast and accurate short read alignment with burrows-whleeler transform" found here, says:


  We evaluate the performance of BWA on ... real paired-end data by
  checking the fraction of reads mapped in consistent pairs and by
  counting misaligned reads mapped against a hybrid genome. 


The data for the real genome aligned to is in table 2.

Which pairs are referred to here? Are these the different software tools aligning the same corresponding reads meaning that they aligned the same sequences to similar locations? Are these paired ends? Or is this something different?
What they are pairing is the RNAseq data with the reference genome: as the legend of the table 2 says:


  The 12.2 million read pairs were mapped to the human genome


These softwares align the same read to the same genome. They aren't comparing if it is mapped to the same location, only how many mismatches has each program.