Friday, March 22, 2019

My BIG Y is ready!

Last Monday it happened, the BIG Y is here after 199 days, just right to be a gift for my 70th birthday!  In my opinion FamilyTreeDna gives much value for money, although they should compensate somehow stumbling in delivery.

Here are some examples showing what you get.  The block diagram is one of the most resourceful apparatus, because it defines my genetic distance by using still unnamed variants.  Here is how it looks:


My match names are erased, but clicking names on your own BIG Y site you see numbers telling how many still unnamed variants differ between you and named kits.



Here the difference is 11 variants and using average mutation rate, 150 years, we can obtain 11/2*150=825 years.   This is an estimation and I need more matches to increase reliability.   
 
It is essential to know the number of unnamed variants, because most youngest markers are unnamed, in my case all younger than 1200 years.  So if you are interested in genealogy, you need to know those markers just now.

Another powerful tool is the chromosome browsing tool, because the read depth varies and FamilyTreeDna tells only the average read depth of their service, not individually.  In some cases it happens that some crucial markers show too few reads and are therefor marked "low quality".   But using chromosome browsing you can see more and rescue your results!  If you are familiar with genetics you can calculate the quality level checking data inside downloadable VCF and  BAM files.  In my case quality scores of BY35383 are for derived allele 24.0287 Phred and the RMS base quality 31.5945 Phred, those values based on FamilyTreeDna's VCF file (Phred conversion to decimal numbers, Wikipedia).  Being even more familiar with genetics you can process the BAM file and pick more information, because the results depends on many run parameter set usually to serve average cases.   Probably you will find out that the probability of those "low quality" variants is 99.9% or even better.  This can save your day if you are genealogist. Two examples here show the difference between high and low quality cases:



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