The majority of X399 motherboards offer eight SATA6Gb/s ports. These ports can utilize RAID 0, 1, and 10. AMD says that the X399 chipset supports up to 12 SATA ports, or eight SATA ports and two SATA Express ports. I have a hunch that adding four more ports does trade off with some PCI-E lanes. However, that is just a hunch based on the board in the image on the left. The motherboard on the left has only six SATA6Gb/s ports, and that is because it has used bandwidth from two SATA ports for two PCI-E lanes, as the motherboard required 10 PCI-E lanes from the chipset, and the chipset only offers 8 PCI-E lanes.
All of this means that AMD has some port flexibility, which means in the future we might even see crazier designs or even motherboards with 12 SATA6Gb/s ports. The reason we haven't already is probably because vendors don't see much demand for more than eight SATA ports, and they would rather use the PCI-E lanes from the chipset for other features.
There are many different types of USB on X399 motherboards, and the motherboard's IO panel pictured above shows many of them. Threadripper CPUs provide eight USB 3.0 ports, and almost all motherboards implement all of them on the rear IO. On the board pictured above, the blue, yellow, and white ports are all USB 3.0.
The white port doubles as the port you use for a BIOS recovery feature, and the yellow ports offer special power delivery features allowing you to disable USB power or increase voltage for longer cables. There is a type-C USB 3.1 port and a type-A USB 3.1 port (in red), and all X399 motherboards offer two USB 3.1 ports from the X399 chipset, they might be used internally or on the rear IO panel.
There are also type-C internal USB 3.1 headers on many X399 motherboards, and they can get bandwidth from a separate controller (on the left) or from the chipset itself (on the right). Typically, when the internal header gets its bandwidth from the chipset, a 3rd party USB 3.1 controller can be found near the rear IO panel for more USB 3.1.
We find two types of USB 3.1 controllers on X399 motherboards; the ASM3142 and the ASM1143. The ASM3142 can accept two PCI-E 3.0 lanes, and is the latest generation controller; I believe the ASM1143 uses PCI-E 2.0 lanes.
AMD's integrated USB 3.1 also requires redrivers, and these are almost always Pericom's PI3EQX USB 3.1 re-driver. Type-C ports also tend to have a switch chip or a switch chip with CC logic on X399 motherboards. The switch is needed for the type-C port to be reversible, as pin assignments aren't mirrored on either side of the connector. The ASMedia ASM1543 (left) is a switch chip with CC logic, while the Texas Instruments HD3220 (right) is a simple switch. In both the cases you see above, the integrated USB 3.1 from the chipset is being routed to the rear IO panel, and one re-driver outputs to the type-A port, while the second outputs to a type-C switch controller.
One vendor went and actually added in ASMedia ASM1464, which are USB 3.0 re-drivers that improve signal quality over longer distances, and they market it for VR. Another vendor (on the right) has implemented a power delivery chip, such as the RT8288A, to help control and increase USB 3.0 voltage levels.
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