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Archiver > GENEALOGY-DNA > 2008-01 > 1199509956


From: "Ron Scott" <>
Subject: Re: [DNA] Chances for Finding Clade-separating SNP
Date: Fri, 4 Jan 2008 23:12:36 -0600


Tim,

"Number of times seen" refers to sequencing to determine the heterozygous or homozygous bases. Ann Turner had mentioned in another thread this link: http://jimwatsonsequence.cshl.edu/about.html, of which contains this statement:

"The number of times each base was seen is reported in parenthesis in a description printed below the triangle. If the description reads "(C:4 T:2)" then it means that this base was sequenced six times: four times it was read as "C" and twice it was read as "T". It is important to understand that our ability to call homozygous bases is limited by the randomness of the sequencing process. For example, if the description reports "(G:0 A:4)" then this means that the base was read four times and all four times it was an "A" rather than the reference sequence's "G". This means that Watson might be homozygous for "A" in this location (he inherited an "A" from both his parents), but it also might mean that we just got unlucky on this base and rolled an "A" four times in a row. If we had read the base a fifth time, it might have shown a "G"."

Ron Scott

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