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VCF File Showing SNP, but Genotyping Column Not Representing Said SNP

I have a VCF file with some lines such as:

  ID    CHR         Pos      Ref   ALT   GT
  1        12     748223      T    C     1/1
  2        12     748433      G    A     0/0
  3        12     754833      A    G     0/0
  4        12     746283      C    T     0/0

The issue is that I don't think I'm quite understanding the Genotyping column. I was under the impression that a 1/1 means that the particular nucleotide has a SNP containing the alternative Allele (so in the first line the alternative is C.) But how come on lines 2,3, and 4, these are clearly SNPS where the individual contains the alternative allele, and yet the genotyping call is 0/0?

Thanks!

vcf
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updated by Ram Ram • written by gtasource gtasource

That is not a VCF file, it's tab-delimited information extracted from one. If this was derived from a multi-sample VCF, it is possible that other samples had a variant in the loci where this sample is 0/0.

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written by Ram Ram

Sorry Ram, the actual file is a VCF file, but what I have posted above is my own extraction of the columns I wanted to discuss in tab-delimited form. I didn't want to post the entire VCF file as this is related to patient information, but I can see how the abstraction I have done was somewhat poor. The actual VCF file has header information, columns related to quality scoring, etc..

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written by gtasource gtasource

OK, that makes sense. Is it a multi-sample VCF?

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written by Ram Ram

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