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FMC116 ADC data having noise at lower internal sampling

I am using FMC116 with FM680. By using the reference design and setting for internal sampling clock. It is found that lower frequencies are having unpredictable noise. for example I have taken 1000 samples with 20KHz 10 times and got noisy signal 8 times as shown below. Is there any way to fix this problem? 

For greater frequencies 60+ MHz the signal gets more stable.

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