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:

Wednesday, March 13, 2019

Iron Age Finns in Southwestern Finland belonged to N-haplogroup

A new article taking place before the study tells that at least four of around twenty samples in a southwestern Iron Age cemetery (Luistari) belonged to the male haplogroup N and no other haplogroups existed.  If we assume an even distribution between females and males, we can say that at least four of ten males carried haplogroup N.  The probability for all ten being N is very high and suggests about quite a dense local population.  The article doesn't give information about detailed haplotypes, so we can't figure the origin or populational connections.   Ten of twenty samples got maternal haplogroups, some showed eastern and some western kinship.  A bit mysteriously the article suggests that maternal haplogroups have more similarity with modern eastern and northern Finns than with modern western or southwestern Finns.  Does this mean that present-day western Finns migrated later?  Or does this mean that Iron Age Finns married women from eastern and northern parts of the country?   Researchers were able to specify some phenotypic details of four men and one woman. They all were blond.   Three of N samples showed mutations linked to the disease Dupuytren's contracture, also called in Scandinavia as "Viking disease".  This is a huge amount, even if we suggest N=20.  Did the Vikings belong to the haplogroup N?


Luistari is a large Iron Age cemetery in Finland with a lot material artifacts like jewellery and weapons and significant even in an European scale including over 1300 burials.



Monday, March 4, 2019

FamilyTreeDna's delivery issues

I ordered my Big-Y kit October 30, 2018 and today I still have no idea about the delivery. I have not either received any explanation from FtDna why I am still waiting for it.  Sure I have asked it.  Expected dates come and go without explanations.  I am disappointed especially because my idea was to open a new blog about Y-DNA and I have now waited for it 185 days.    If I only could have known what I know now I would have had choices  Now I have not. They can keep me hanging as long as it takes.