PCIe not detected in custom carrier board

Autonomous Machines Jetson & Embedded Systems Jetson AGX Xavier
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We were using jetson AGX Xavier industrial, with our custom designed carrier board in that board while checking for PCIe link up internal C5 controller/bridge was not coming in lspci command. but if we put Jetson AGX Xavier Carrier board it’s detected.

  1. what are the conditions need to check for detection of PCIe bridge?
  2. PCIe Reference clock 100MHZ is free flowing clock?
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It sounds like a hardware problem, is this still an issue to support? Any result can be shared? Thanks

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