A basic concept question: In Plink analysis, the genotype "T" will be replaced with "T T" My question is not why computer need such an input format, my question is a pure biology question. Why there is only one genotype here?
Thanks.
I'm a little confused by your question, but:
PLINK is designed to analyze organisms with two copies of each chromosome (excluding sex chromosomes as a special case). At any point on the genome, there will be two genotype values, one for each copy. Thus, PLINK takes genotypes of the form AG or GG rather than A or G. If the organisms is homozygous T at a given location (both chromosomes have a T at that locus) then you would have two copies of T, represented as TT.
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I suggest you start with Griffith et al. "An Introduction to Genetic Analysis", available for free at http://www.ncbi.nlm.nih.gov/books/NBK21766
I have difficult to understand the concepts. Each chromosome(DNA) has two chains.So genotypes AT comes from each chain?
Each chromosome has two strands, and each individual has two chromosomes. The T T means that on chromosome N, copy 1 at that position there is a T. On chromosome N, copy 2, there is an N. For each SNP only one strand is reported (and because DNA is anti-parallel and complementary we know the other base on each chromosome).
Can you give me some link about anti-parallel and complementary? I am really confused about it. And even I don't know the concept of copy 1 nad 2. Let me give you an example, individul say "ardmore" has two chromosomes. In "ardmore"'s chromosome 6 bp position from 32,000,000 to 32,000,004 the genotype in strand 1 are "AGCT", then how about strand 2? Then how about in the other chromosome. I need an example, many thanks!