Hello, I tried to find the information to be 100% sure, but I couldn't find it. We are investigating a SNP and its impact on Alzheimer's disease. We have identified our SNP and obtained a table with the following information: original base: C; new base: G. We were wondering what the values 0, 1, and 2 correspond to in the column associated with each patient. Thank you very much.

Created by Vincent Hervé Vincent_Herve
Hi @Milton, Yes, I've gotten some clarification. Per the manuscript referenced in the wiki (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307898/), they used MACH for imputation. Per the [MACH documentation](https://csg.sph.umich.edu/abecasis/mach/tour/imputation.html), the dosage is the first allele. For this file specifically, because it was generated with MACH, the dosage counts copies of the first/reference allele (C), not the ALT allele. So a value of 2 means C/C, not G/G.
Hi! Please, any news for me? I am checking another SNP, rs3825924, and I see the same pattern. In the .dosage file we have G in the second column and this is the most common allele, with A in the third column, which is the less common variant. Most part of values in the line of this SNPs are 2 (1146 to be exact). In the .bed file we have the inverse, most of the values are 0 (also 1146).
Hi @Milton, my interpretation would be G/G, but I can understand how the frequency of that genotype in the participant population may be unexpected given the [general population frequencies](https://www.clinpgx.org/variant/PA166157260). Let me see if I can follow up with someone who knows more about how these files were generated.
In the three first column of the file .dosage, we have the SNP (rs680055) in the first column, a C in the second column and a G in the third column. This is followed by the imputed dosage described above, that is 2 in the great majority. In this case, a 2 means what in case of genotype? CC or GG? Thanks, Milton
Hello @Vincent_Herve, Thank you for your question! Given two alleles of a SNP — in this case C (reference) and G (alternate) — there are three possible genotypes: CC, CG, and GG. An imputed genotype dosage is estimated as 0·P(CC) + 1·P(CG) + 2·P(GG), giving a value between 0 and 2. So in integer terms: **Value** | **Genotype** 0 | C/C — homozygous reference 1 | C/G — heterozygous 2 | G/G — homozygous alternate This forum post may provide you with further context: https://www.biostars.org/p/75689/#98336. Let me know if I can provide further clarification and I can loop in a Sage scientist with more domain experience to explain further. Best, Emma

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