I wanted to include screen shots with this but Yahoo won't let me so if some of the references make you?confused see this document in the files section where I will include them.
Okay, I¡¯m going to cover the BigY match screen for those who use it or are confused by it. First off, have very little faith in anything you find on this page. It is full of garbage. There are little nuggets of truth to be gleaned from here so it isn¡¯t a total loss, but unless you really know what you are looking for it isn¡¯t going to be helpful at all. When you get your BigY results make sure that the first thing you do is upload your vcf file to the U106 group to have them analyze it. If that statement sent your head spinning let me know you need help and I¡¯ll give you step by step directions for getting that file and I¡¯ll upload it for you. It¡¯s that important that you do this step!
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So back to the page that is just 99% confusing and mostly plain wrong. The first thing you¡¯ll see when you go to your? BigY Matches tab is a list of people you match to and in the columns across from their name the number of Shared Novel Variants, Known SNP Differences, and Non-Matching Known SNPs. It defaults to show you the match that you share the highest number of Shared Novel Variants and the fewest known SNP differences with. So, if you start out with the first person on your list and click on the number in the Shared Novel Variants column it will open a new screen for you (see examples in file section if needed). On that screen, you will see what novel variants (meaning unnamed SNPs) you share with your match, what novel variants belong just to you, and what novel variants are only his. Let¡¯s start with the shared novel variants. So, I go to the number 32 shared novel variants that the match at the top of my list has and click on it and I find that we actually share 19 SNPs on the pop-up screen. What?!! What happened to the 32 SNPs we share? Who knows? This is the first of many bad pieces of data on this screen. And checking all my matches almost every one of them has a bad number on the first screen.
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So, let¡¯s deal with that second screen; the one that popped up. The important columns on this screen are the Reference and Genotype columns. First off, know that outside of FTDNA they are going to probably refer to these values as Ancestral and Derived. What this means is that there is a reference sample they use that we all get compared against. So we are looking for any changes or mutations since that reference/ancestral value. If there is a change that will become the Derived value (what it changed to). So if the reference/ancestral value was a G and we now have a derived value of T you will be deemed positive for that SNP. So look down the columns Reference and Genotype and note all the SNPs that have changes. On the screen I posted you¡¯ll only find two SNPs that have changes (the first two) and all the rest are still at the ancestral value. So there is nothing novel about most of these. In fact, in the whole list of 19 that my match and I share only 3 are valid. So we just went from a screen that said 32 variants, to a screen that said 19 variants and when we look at them all only 3 are real. That¡¯s why I say don¡¯t pay attention to those novel variant numbers on your first screen. So one more thing I want to point out, and this is why we have the guys at U106 analyze our results, those 3 variants we share are not very good SNPs and so U106 doesn¡¯t even count them. So what my match and I share just went from 32 to 0.
Now, on the Known SNP Difference and Non-Matching Known SNPs, those are pretty much true. If you show 1 Known SNP Difference in your column then it will list that Known SNP in the Non-Matching Known SNP column. You can use it to rule out matches right away by seeing something like Z343 as a non-matching SNP and you will know that this person is not on the same branch as yourself.?
But it¡¯s hard to keep all those SNP names in your head and know what SNPs matter and what don¡¯t. So don¡¯t use these columns unless you really want to. Instead, go up to the top of your screen and use the ¡°Filter Matches by Subclade¡± button.?Press the drop-down button and it will show you about four different SNPs above you on the tree and at the bottom it will show you yours.?You can click on any of these and it will show you the people in those subclades. There is a number over to the right and it is how many people are in this subclade. So the fastest way to see who you match is to go to this button. Sometimes it doesn¡¯t populate for me right away so I keep refreshing until it does.
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The data in the tabs for novel SNPs for just you and just your match are fairly true. The problem with some of them is that, again, they might not be quality SNPs so they won¡¯t necessarily get counted in the U106 BigY Spreadsheet but I find the data good to have.
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One other thing to know about this match screen is that you can go all the way over?to the right where it says Match Date and if you click on it, the screen will resort by date (it¡¯s slow, give it some time). The first click it will sort by oldest match date and then click it again and it will sort by newest match date. So if you want to see if any new match has come along this is the fastest way to find them. Actually, all these different columns can be chosen as the one to sort on but you probably don¡¯t need to do that.
So, that ends our little tour of the BigY Match screen. If you have questions or comments let me know. This is the tool FTDNA gives you for seeing your data so know how to use it and know when to ignore it.
