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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 benchmark on various kernels and distributions.
I have added a heatsink and fan to the RPI3, to allow for non-throttled performance.

Debian bootstrap is used for building bwa, so the same binary is used for all distributions

debootstrap --no-check-gpg --variant=buildd --arch=armhf unstable arm32-sbuild http://ftp.debian.org/debian
debootstrap --no-check-gpg --variant=buildd --arch=arm64 unstable arm64-sbuild http://ftp.debian.org/debian

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 Native env 32bit chroot env 64bit chroot env
Raspbian (32bit) stock 4.9.24-v7+ 32bit 355.260 351.479 N/A
Raspbian (32bit) self-compiled 4.10.15-v7 32bit 355.748 351.983 N/A
Raspbian (32bit) self-compiled 64bit 4.10.15-v8 381.616 375.793 294.206
openSUSE (64bit) stock 64bit
pi64 (64bit) stock 64bit