I believe it ships with L4T (Linux for Tegra) R27.0.1. This is Ubuntu with NVIDIA’s hardware accelerated drivers on top of it, but is otherwise just Ubuntu. This isn’t a very reliable release, it is recommended to flash to R28.1. R28.2 has a pre-release out, but you might want to consider R28.1 the current stable release.
This can be flashed on command line with any x86_64 Linux host by means of the driver package plus sample rootfs over the micro-B USB cable when the Jetson is in recovery mode. You can also use the front end JetPack3.1 (3.2 is the pre-release). The advantage is that JetPack can also install additional packages on both host and Jetson, but must be used from either Ubuntu 14.04 or Ubuntu 16.04 hosts. In this latter case you also need to connect wired ethernet for the package installs…if you choose just packages and not flash, then you don’t need the micro-B USB cable and the Jetson would be booted normally.
Note that a VM host has problems and requires a lot of work at times to make it work for flash.
The carrier board has one full-sized USB connector (capable of USB3), and one micro-USB OTG (“On The Go”) USB connector. The OTG connector uses a type-B USB cable when in recovery mode…but if running normally and you use a type-A USB cable, then this is an ordinary USB2 port.