The exact definition of “mapped in proper pair” depends on the aligner and the options used for mapping. In
bwa mem, the algorithm automatically infers the general read orientation and the insert size distribution from a sub-sample of reads. It should have printed it in the standard error output when you ran the program. Pairs with different read orientation or with insert size too high or too low compared to the averaged insert size distribution are considered not mapped in a proper pair.
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