GQ and PL fields

[mashid]

Hello.

For GATK GQ value is equal to the second smallest PL (https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format). But this is wrong for our result. Could you explain how GQ and PL are calculated and related?

Example of our result:

Best regards, Maria