Family Tree DNA’s Y-500 is Free for Big Y Customers

Did you notice something new on your Y DNA results page at Family Tree DNA this week? If not quite yet, you will soon if you have taken the Big Y test. There’s a surprise waiting for you. You can sign in here to take a look.

The first thing you might notice is that the Big Y has been renamed to the Big Y500. However, the results I want you to take a look at aren’t under the Big Y500 tab, but on your regular Y DNA Y-STR Results tab. Click to take a look

In the past, 5 panels of Y DNA STR markers have been available:

  • Panel 1 – 1-12 markers
  • Panel 2 – 13-25 markers
  • Panel 3 – 26-37 markers
  • Panel 4 – 38-67 markers
  • Panel 5 – 68-111 markers

Now, a 6th panel has been added:

  • Panel 6 – 112-550 markers

However, there is a difference between the first 5 panels and the 6th panel.

Why is it Called the Y500?

If there is a total of 550 markers reported, why is this product called the Y500?

That’s a great question with an even greater answer.

Family Tree DNA actually tests for a total of 550 markers. Values for markers between 112 and 550 are provided FOR FREE when you take a Big Y test.

Family Tree DNA guarantees that you will receive at least a total of 500 markers, or they will rerun your Big Y test at no cost to you to obtain enough additional markers to reach 500. (The 500 number assumes that you have all 111 STR markers. If you have not tested all of the STR panels, the number will be lower by the number of STR values you haven’t tested. This means that if you took the Y67, but not the Y111, your 500 guarantee number would be 500-44, where 44 is the number of markers in the Y111 panel that you have not yet ordered.)

The best part?

The markers above 111 are ENTIRELY FREE with a Big Y test – for both existing customers who have already taken that test, and all future customers too. Yes, you read that right. If you took the Big Y previously, you are receiving the markers in panel 6, 112-550 absolutely free.

How does it get better than free?

The Big Y Uses a Different Technology

There is a difference between the first 111 markers and the markers from 112-550, meaning that they are read using different technologies

The results for the first 111 STR markers are produced using a technology that targets these specific areas and is very accurate.

The results for the 112-550 markers is produced using next generation sequencing (NGS) on a different testing platform than the Y-111 results. NGS, utilized for the Big Y, scans the Y chromosome rather than targeting specific locations. This scanning process is repeated several times, with values at specific locations recorded.


Using NGS technology, your DNA is scanned multiple times, with the number of scans, such as 25 or 30, referred to as the coverage level. The goal is for multiple/most/all scans to find the same value at the same location consistently. Because of the nature of scanning technology, this sometimes doesn’t happen, for various reasons, including “no-calls” which is when for some reason, the scans simply can’t get a reliable read at that location in your DNA. No calls are typical and occur at low levels in everyone’s scan.

Here’s an example from a Big Y scan viewing the actual results using the Big Y chromosome browser.

The blue bars are forward reads and the green bars are reverse reads. Dark blue and dark green bars indicate high quality scans. Medium blue and green are medium quality scans and faintly colored bars indicate poor quality. If you take a look at where the little black arrow at the top is pointing, you can see that a T is the expected value at that location.

When the expected value as determined in the human reference genome is found at that location, nothing is recorded in that column. However, when a different result is discovered, like A in this case, it’s noted and highlighted with pink. We can see that there are 5 As on forward and reverse strands of high quality, then a low quality read, 6 more high quality reads, followed by two reads that show the expected value (nothing recorded) and then three more high quality A reads.

The goal is to determine what actual value resides at that location, and when that value is determined, it’s referred to as a “call.”

For a “call” to be made, meaning the determination of the actual value in that position, the person or software making the call must take several quality factors into consideration.

In this case, the number of high quality reads indicating the derived (mutation) value of “A” allows this location to be definitively called as “A.” Because several other men previously tested have A at this location, a SNP name has already been assigned to this mutation – in this case, A126 in haplogroup R.

However, if you look to the right and left of the arrow to the next two browser locations that contain mutations, you can see in both cases that there are less than half of the column locations that are marked as pink with derived values (mutations), meaning those not expected when compared to the reference model.

These types of locations which are neither clearly ancestral (reference model) nor derived values are when value judgements come into play in terms of deciding which value, the ancestral or derived, is actually present in the DNA of the person being tested.

Some people will call a SNP with only one mutation reported out of 20 or 30 scans. Some people will call a SNP with 2 scans; some with 5, and so forth. Generally, Family Tree DNA uses a minimum threshold of 5 high quality scans to call a mutation value.

Now, let’s talk about how STR values, meaning results displayed in those locations between 112-550, are found in your Big Y NGS data file. You can read about the difference between SNPs and STRs in the article, STRs vs SNPs, Multiple DNA Personalities.


Short tandem repeats, known as STR values, are the numbers reported in your STR panels. These are stutters of DNA, kind of like the copy machine got stuck in that one area for a few copies.

For example, in haplogroup R, for this person, the value of 13, meaning 13 repeats of a particular sequence, is found at marker DYS393.

Repeated sequences are in essence inserted in-between SNPs in some DNA regions, and the number of repeats reported in STR marker panels is the number of stutters, or repeats, of a particular repeated sequence.

That sounds simpler than it is, because how to count a sequence isn’t always the same. Let’s look at an example showing 20 consecutive DNA positions.

The actual values are shown in the value row. However, these values can be counted in a number of different ways. I’ve also added a “stray read” at location 13 which causes confusion.

At location 13, we show a value of G which does not fit into the repeat pattern. How do we interpret that, and what do we do with it?

The repeat pattern itself is a matter of where you start counting, and how you count.

I’ve color coded the repeats with blue and yellow. Incomplete repeats are red. The stray G in location 13 is green, because it breaks the repeat sequence.

In example 1, we start counting with T in position 1, and there are clearly 3 repeated groups of TACG before we hit our stray G in position 13, which stops the repeat pattern. However, after the stray G, there is one more full repeat sequence of TACG. Do we ignore the G and count the 4th TACG as part of the group, or do we count only the first 3 complete TACG sequences? The total number of repeats could be counted as either 3 or 4, depending on how we interpret the stray G in location 13.

In example 2, we start counting with the GTAC, because I was simulating a reverse read where we start at the end and work backwards. In this case, we clearly have 2 reads, then our stray G which occurs in the middle of a read. Do we ignore that stray G and call the rest of the blue GTAC surrounding the G as a repeat? That blue repeat group is followed by another yellow group. Do we count it at all, or do we simply stop with the marker count of 2 because the G is in the way and breaks the sequence? This repeat sequence could be counted as either 2, 3 or 4, depending on what you do with the G and the following sequence group, both.

Examples 3 and 4 follow the same concept and have the same questions.

All STR sequences face the issue of where to start reading. Where you begin reading can affect the number of repeat counts you wind up with, even without our stray G in position 13.

STR markers obtained from NGS sequencing face this same challenge, but it’s complicated by the issue of no-reads and the call variance that we saw in the chromosome browser where the same location is sometimes called differently on different scans, meaning we really can’t tell which is the actual value. What do we do with those?

All of this is complicated by the fact that some regions of the Y chromosome simply do not produce valid or reliable information. Different (groups of) people define this unreliable region as starting and ending in different locations. Therefore different people analyzing the same information often arrive at different answers to the same question or use marker locations that others don’t.

I suspect all of this may fall into the category of trivia you never wanted to know, but now you’ll understand why you may find different (sometimes strongly held) opinions of what is “right” when two geeky types are arguing strongly about a particular STR value as your eyes glaze over…

Here’s the bottom line – if you’re using results called by the same vendor, you don’t have to worry about whether you and someone else are being accurately compared. You and everyone else at that vendor will have your results reported using the same technology and calling methodology.

Family Tree DNA has always taken a more conservative approach, because they only want to report to customers what they know to be accurate.

You will not see low confidence values on your reports, nor calls from an unreliable region. Genealogists cannot reach reliable genealogical conclusions using unreliable data.

The Big Y 500

Because of the nature of scanned STR results, Family Tree DNA can’t guarantee that you will have a reliable read at every location. In fact, few people will have values at every location. The technology for the Y-111 markers provides a very high level of accuracy and Family Tree DNA will provide results for every 1-111 location unless you actually have a deletion, meaning no DNA in that location. However, the values of markers 112-550 are taken from the Big Y NGS scan.

Therefore, some Big Y customers will have a few markers above 111 that show a “-“ instead of results, such as FTY945 and FTY1025, shown below. A value of “0” found in markers 1-111 means that there is actually no DNA in that location, and it’s not a read error. No DNA at a specific location is heritable, meaning it can serve as a line-marker mutation, while a “no call” means that the scan couldn’t read that genetic address. No calls cannot be compared to others and should be ignored.

Before someone starts to complain about having markers with “no reads,” remember that Family Tree DNA is providing up to 439 additional markers available FOR FREE to customers who have taken (or will take) the Big Y test.

That’s right, there is no charge for these new markers. You are guaranteed 389 additional markers, but you may actually receive as many as 439, depending on how well your DNA reads. The kits I’ve checked have only been missing a couple of marker values, so these kits received 437 additional markers, far above the guaranteed 389.

Right now, matching is not included for the 112-550 markers. Matching above 111 markers may be challenging because while Family Tree DNA does guarantee that you’ll have at least 389 new marker values, those won’t be the same markers above 111 for everyone. In a worst-case scenario, you could mismatch with someone on as many as 100 markers above 111 panel, simply because both you and the person you are matching against are both missing 50 different markers each, for a total of 100 markers mismatching.

Additionally, not everyone has tested all 111 STR markers, and you will receive your 112-550 values if you have taken the Big Y test regardless of whether or not you’ve tested all 111 STR markers.


Matching on the first 111 markers is reliable because you will have an accurate value, even if the value is 0. Having no DNA at a specific location is a valid result and can be compared to other testers.

With different markers between 112 and 550 missing for different men, matching becomes very tricky. Specifically, how do we interpret mismatches? How many mismatches to we allow to still be considered a reasonable match?

Matching is an entirely different prospect when integrating the markers between 112 and 550 into the equation with a potential of up to 100 mismatching locations in that range simply from no-reads.

I had presumed that Family Tree DNA would offer matching on these additional markers. Presume is a dangerous word, I know. Matching is not offered right now, and given the complexities, I don’t know if matching as we know it will be the future or not, how reliable it would be, or how Family Tree DNA would compensate for the missing STR information that differs with each person’s test.

Furthermore, I’m not quite sure what they would do with two men who haven’t both tested to the same STR level, meaning panels 1-5, but have taken the Big Y so have values for 112-550.

Big Y Purchases

Here’s the status of Big Y tests, today:

  • New Big Y purchase if you have done no Y DNA testing at all – you will now be able to purchase a Big Y without having to previously purchase any STR markers. The 111 STR markers are now bundled into the Big Y purchase, which makes the Big Y appear more expensive than before when the STR markers had to be purchased separately before you could order a Big Y test. The Big Y plus all 111 STR markers is now $649 during the DNA Day Sale, regularly $799.
  • Already tested through 111 STRs – the Big Y is only $349 on sale right now, and $449 regularly, both significantly discounted from just a few months ago.
  • Existing customers who have taken some level of Y STR test but not the Big Y – will have to upgrade their STR test to the 111 level when ordering the Big Y. Those tests are discounted appropriately, shown in the table below.
  • Existing customers who have not tested their STR markers to 111, but have already taken the Big Y – will receive marker values from 112-550. However, they will only receive the Y STR markers below 112 for panels they have paid for. This means that if you have only tested to 37 markers, you will have results for locations 1-37, not for 38-111, but will have results for locations that read from 112-550. This would be the perfect time to upgrade so that you have a complete marker set.

Right now, Family Tree DNA is having their DNA Day Sale and it’s a great time to purchase a Big Y or to upgrade your STR markers if you don’t have the full 111. The sale pricing shown is valid through April 28th. You can click here to order.



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Thank you so much.

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52 thoughts on “Family Tree DNA’s Y-500 is Free for Big Y Customers

  1. FYI… FTDNA has a “known glitch”… I tried to upgrade one of the kits I manage from Y-111 to Big Y on the FTDNA website. The discount price does not display ($449 upgrade is supposed to be $349 right now). If you wait for approximately 20 minutes on hold for a live FTDNA customer service person, he/she can apply the discount over the phone for you, and email a payment confirmation after the fact.

      • I did not place the order online at all, after realizing the discount wasn’t showing up on the website, so the only email I received was the order confirmation after placing the order over the phone with a customer service person (he applied the discount manually, so I never received any coupon.)

  2. Hi

    It says $459.00 for the Big Y 500 upgrade, nothing on there about free.


    On Mon, Apr 23, 2018 at 11:04 AM, DNAeXplained – Genetic Genealogy wrote:

    > Roberta Estes posted: “Did you notice something new on your Y DNA results > page at Family Tree DNA this week? If not quite yet, you will soon if you > have taken the Big Y test. There’s a surprise waiting for you. You can sign > in here to take a look. The first thing you mig” >

    • If you have ordered the Big Y test in the past, the upgrade to the 500 STRs is free. If you order the Big Y test now, the 500 STRs are provided for free. In other words, those STRs are free as a benefit of having ordered, or ordering, the Big Y test which is now called the Big Y500.

  3. I enjoy reading your articles, but what is a marker? This is all new to me, Halo groups, HVR, too have no idea! What is a Chromosal browser too? My daughter did the DNA and so did I but was there really a need for both of us to have the same MtDNA test done, since we should matched? So much to learn , will just keep reading your info until some of it sinks in! Thanks!

    Sent from my iPad


  4. Confused. Email says both. Is the big y 500 free or not? Roberta do I get free or do I need to pay?

    John Szaton

  5. Am I missing something here? What is the purpose of markers 112-550 if they’re not used to identify matches? What’s their practical application as a research tool?

  6. Question… I ordered the big y combo pack(111 + big y). I was going to take them both myself, but now I am wondering if I should have my father take them instead? Would this get me more bang for my buck? In other words, wondering if I’ll get deeper/more precise/less mutated results if I skip my generation. Or does it not matter?

  7. I took the BigY shortly after it was first available, and I had already taken Y-111. I’m missing 56 markers in panel 6, which would seem to be beyond their threshold, but I’ve heard nothing from FTDNA.

      • Turns out their FAQ indicates that tests passing quality control will receive at least 389 sequenced STRs in panel 6, which means someone could be missing as many as 61 of the new markers. []

  8. Nice to have this new 112 to 550 markers for and for free!
    But to what can we use it?
    I have not got any good answer about that from any body. The only thing I got is way bouther it is free!
    But I realy want to know what use we have about them and what futher use and help in our ancestry research we have whit them. Or are this just a neet thing to have for them that find the value to look at mutation in different positions?

    In the SNP part of BigY I only have one match in all of the 5 levels in the tree when BigY was updated. It is my own father. Befor the update we at least saw one other that is ouher currently closest match. Hi is in a haplogroup branch just one step over us in the tree. We have him as GD5 at Y67 level and in the old BigY we had him as a match and we three build that group he have stayed in. Me and my father got som more SNP named at YFull and with an futher analys at FTDNA thay place us (father an me) in this on step lower posision in the tree.

    But If I look att the TMRCA at the tree I have at BigY today I would not have any ancestors that have been tested within about 2700 years! Then I’m is in a prity big tree sinse I’m in I1 (I-M253) and under the I-P109 brash of it. So it is not a unknown tree. So I do not feel that BigY have given me anything at FTDNA more then a new brash in the haplotree and a terminal SNP. Then some matches at Y67 that is GD5 and futher away even if my father and I have Y111.

    • These tests are gift that keep in giving, both as more people test and more features are added. I am currently working with some 112-550 matches in a known family group to do some analysis.

      • I´m in a bit of hurry. My father an I don´t known the my grandfathers father. and my father is over 85 years old so I probable have not so many years on me to find the grandgathers father before hi is gone. *He was werry il at Christmans and nearly dead then!
        So I´m a bit hurry on this and have no clue to find my grandfathers father even if it is in a rather small area in Sweden. I have enen try to get help from very experience peoples in my sorunding with out any results. Even if I seams to be quite experence by my self according to others.
        So I have a last change to find this grandfathers father before my father is gone!
        So I realy try to find all connection bot even If I have spend all many I can on all test that FTDNA have I have not get any clue to find the ancestors on that side that is identify. So my father and I have both taken FF, Y111, BigY and mtFull Sequence.
        And! Yes I know that mtFull Sequence dos not help in the grandfathers fathers line. It is in my fathers mothers line! 😉 But also that is inristning because hi is also alown in that haplogroup even if it is prity large as W1-T119C and non matches over HVR1 level! Even if it is a well known area with blacksmiths in a small known area in Sweden!

        And Yes I know that more peoples need to test in this areas that is in prity small area within about 50 km (about 30 mils In you mesurment).

        So I realy have got nothing for my father even If I have spend about $1000 at only his testning at FTDNA. This exept all the test I have done!

        So realice that I realy want to know everything that can help me to solve ouer mysterium with the grandfathers father. So I realy want to know what this with BigY-500 is helping me to get futher or if it is just nonsense that is for peoples that is intrassling to look at DNA values whit out any realy help to find ancestors!

        And who is Bob that I seams to replying to! I have a conversation whit Roberta at this site what I know! But I shows up as “Leve a Reply to Bob” insted!

    • I also don’t quite see the advantage of the extra markers (yet). Maybe it’ll be of some use some day to some of us.

      But what I really dislike about the new Big Y is the obligation to buy 111 STR. I was thinking of taking Big Y before sale started, hoping they would go down close to 400$. With my current 37 STR, I now only get a discount of 26$.

      I currently have really few matches, and I’m just not interested in getting more markers. Plain old Big Y on the other hand would have given me my exact position in tree, in any future version, plus my modest contribution to advance science.

      With that new sales model, I doubt that I will ever do NGS test. So – rather a disappointment. And the feeling that they are trying to push STR tests, at the cost of scaring off folks like me.

      • You may look at this in such a way: previously on sales Big Y costed 475$. That meens 37 to 111 STR upgrade costs you 74$ now (instead of 220$) and still having Big Y discount.

  9. Weeks have gone by while I have tried to choose next Y tests for my son. Taking your advice
    I Upgraded the DNA-Y67 test and ordered discounted Y-DNA111 and the Big Y-500, as well
    as the sale price Family Finder. Total sale price, $508.00.. I believe this covers next tests
    recommended, correct? I have not ordered the Full Sequence MtDNA for him, as I am asking my daughter, age 70, to take it, and am wondering if her results could be transferred to his results page?? I have my MtDNA on record at Family Tree DNA, as I authorized the transfer of test
    results when I took the Geno 2.0 test through National Genographic. When I recently began an account wuth FTDNA and ordered a Family Finder Kit, my Haplogroup results appeared and
    I am classified as V-C7211.. When John’s Big Y-500 or Y-111 test results come in will he
    be grouped under Abraham, Moses. John +Elizabeth C. ??? My son John is a descendant of John and Elizabeth Chisum and their son, Joseph Estes, b. Abt.1780/90 in Tenn. (married Ritty LEE) died in Mt. Vernon, Jefferson Co.,Illinois in 1846. Really enjoy your ‘Ancestor’ stories !


  10. Thanks Roberta. I thought that would be the case. Correction on Haplogroup listed—
    Should be V-C72T1 (The last 1 looks like an exclamation point, but am not sure, and wonder if that is correct. What would this symbol mean?..

  11. I’m considering a Y-111 test–unfortunately, I missed the April sale prices. Will the Y tests likely be on sale again in June around Fathers Day?

  12. Hello, Miss Roberta. About a weeks ago i received Big Y-500. Today i have 560 STR’s from Y111 STR’s plus Big Y-500. My Y DNA Haplogroup is O-F204 (M133) or CTS11856 / CTS5492 / CTS5063. What the benefit for me to have around 560 STR’s? It can help a Geneticist to determine a new Haplogroup? I really don’t understand with this case 🙁

  13. I have done some experimental pairwise STR marker TMRCA age to the common ancestor with both FTDNA y-561 and YFull y-587 set’s and found FTDNA set to be the most accurate and better than the y-111 set.. There is mathematical ways to adjust for different number of markers. At this time, I have not done enough tests to verify the accuracy of this method. I need to find a better way to automate the process, but at least it shows some promise that there is a useful purpose for these new STR Markers.

      • The YFull set does vary widely, but the FTDNA set in a STR Marker Pattern analysis study we did with 6 members of the same set of sub-clades only 17 STRs showed any differences at all. FTDNA has more experience with using sets of markers. YFull always reports all STR Markers, which is technically correct, but the researcher has to choose amongst them which one to use.

        Both YFull & FTDNA sets help in predicting the sub-clade the customer maybe in, through STR Marker Pattern Analysis.

        There is so much negativity about these additional STR Markers. I and several other Administrators are trying to convince our members that they can be extremely helpful. It just takes time, because they are new. Same as the y-111 set, when it came out.

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