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Since there is no official 64bit Rasbian distribution for the Raspberry Pi 3, there has been a lot of discussion if a 64bit version would actually give any performance benefit.
I try to answer the question by performing BWA-0.6.2 on various kernels and distributions.
I have added a heatsink and fan to the RPI3, to allow for non-throttled performance.

pi64: https://github.com/bamarni/pi64 openSUSE: http://download.opensuse.org/ports/aarch64/tumbleweed/images/openSUSE-Tumbleweed-ARM-XFCE-raspberrypi3.aarch64-Current.raw.xz


Dist Kernel Kernel-arch GCC 32bit 64bit
Raspbian stock 32bit N/A
Raspbian self-compiled 32bit
Raspbian self-compiled 64bit
openSUSE stock 64bit
pi64 stock 64bit