What is the relationship between the per-base sequence quality of a FASTQ file and the QUAL of a VCF file
I have a FASTQ file whose quality is summarised in the following graphs.
I understand that if a base has a quality score of 30, that means that I have a 99.9% of accuracy that this base has been called correctly. However, when looking at the VCF file generated with the same FASTQ file, I got this
what is the average quality score of the variants called by the different pipelines I have developed. This average QUAL is (according to VCF documentation ) the same Phred-scaled quality score but this time for the assertion made in ALT. So, this really means that accuracy of this bases on average is 100% (because 60 is already 99.9999%)
Is this interpretation correct?
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