If you run your sketch (e.g. blink) device manager will say Micro on COMx in the ports section of the device manager; if your board is in bootloader mode it should say something like Micro (bootloader) on COMy or Leonardo (bootloader) on COMy in the ports section of the device manager.
I've never read about a board in bootloader mode that identifies itself as a serial device in the ports section of the device manager; it does not mean that it's not possible but I consider it strange.