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When using an LR card the USB port can be used only for power delivery, it power will be switched off by the CPU. It cannot be used together with an LR card.  

Automotive connector usage

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SIM card connectivity

• MiniPCIe 1 LR (top slot) supports PCIe and USB 2.0 cards but is shared with the USB 2.0 type A port (can use either the USB port or miniPCIe slot at the same time). It can be used only for SIM slot #1.
• MiniPCIe 2 LTE (bottom slot) supports only USB (2.0 and 3.0) miniPCIe modems (no PCIe support). Uses SIM slot #2 and SIM slot #3. By default uses SIM slot #2. The sim cards can be switched in ROS.
• USB 2.0 type A port (can only be used if miniPCIe 1 is not used). If using LR, the USB will be turned off.
• To use the top miniPCIe slot with a USB type miniPCIe card, switch the USB connections to the miniPCIe slot: /system routerboard usb set type=mini-PCIe This will disable the USB 2.0 port on the front of the unit.

Insert the SIM card into the top slot by a chip on the SIM card facing down. Bottom slots – with the chip facing up.

Please check if you are using the correct SIM slot. For the modem inserted in the bottom mini-pcie slot, you need to use either sim slot 2 or sim slot 3. And the used sim slot needs to be selected in RouterOS.
CLI command to select the sim slot: /system routerboard modem set sim-slot=2

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