Am a beginner to genomics etc, so apologies for a trivial/strange question. When looking at a 23andMe dataset, the first variant listed was the following:
rsid chromosome position genotype rs548049170 1 69869 TT
However, when I create a VCF file from this dataset, I see the following:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE 1 69869 rs548049170 T N . . . GT 0/0
Why is it considered a variant when the genotype (TT) is the same as the reference allele? Surely this isn't a variant then, so why is it included in the 23andMe data? Furthermore, everywhere that a situation like this occurs in the VCF file, the ALT column is set to N. What does this mean?