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
|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 4.10.15-v8||64bit||381.616||375.793||294.206|
|pi64 (64bit)||stock 4.11.0+pi64-v8+||64bit||280.148||360.715||278.164|