I am pasting the examples below.
chr1 1488959 . TG T 293.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.064;ClippingRankSum=-0.268;DP=58;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.71;MQ0=0;MQRankSum=0.268;QD=5.67;ReadPosRankSum=-0.755 GT:AD:DP:GQ:PL 0/1:29,27:56:99:321,0,344
Here, it states that the variant is heterozygous with the DP 56 and ref count AD 29 and alt count AD 27. Here my understanding is, 29 reads are having "TG" in them and 27 reads are having "T" in them. So we refer them as heterozygous. Am I correct?
Also, if ref-AD is 4 and alt-AD 52, what will be the genotype? still heterozygous?
What is the threshold value for Mapping quality (293.73) ? What is the good mapping quality score or bad mapping quality score?