My Haplogroup is A11134. I share that group with 7 people of Hartley Surname (though one changed his name to Hartley, partly as a result of the testing). An 8th BigY tester in the A11134 group has Nutter heritage. His is the most recent results. Here is where Nutter is under A11134 in the lower right below. This shows he shares A11134 with two other Hartleys
My previous analysis of Nutter’s results and other Hartley results has left me with some questions that I would like to look into further. Previously, I had been working on this list of Variants:
BAMsAway
This is a Chrome Browser extension that looks into positions on the YDNA BigY test that FTDNA may not provide information on. Recently, I was looking at Nutter’s Private Variant with Position number 5672076. It appeared from my download that FTDNA had not tested that location for me. However, using BAMsAway, I see this for that position looking at my results:
This shows that clearly I was negative at this position. While I’m at it, I’ll check all my Variants that I previously thought were not covered by my test:
I’m not so concerned about the last three testers, as I know more about their genealogy back to the 1600’s. However, the first two positions that I checked were clearly negative, so that is a good sign.
6906758
This position is interesting as Nutter showed that this was one of his Private Variants at YFull based on his non-FTDNA testing. I show negative for the Variant:
Here is what Nutter’s results show:
I am not sure why Nutter’s results did not show this as a Private Variant at FTDNA. This may be something to look into further.
BAMsAway ‘No Reads Found’ at 13807922
Here is the first Variant that I looked up with no reads found:
Here is how the Browser displays:
However, the position number does not show. I suppose this would make sense if there were no reads. I showed this result in blue on my spreadsheet:
I had previously shown this as not tested and ‘no reads found’ is the same thing. This is the first BAMsAway result that confirms what I thought to be the case previously. Here is what Nutter shows at that position:
Here there were only 2 good reads. Many assume that 10 good reads are needed by FTDNA, so this Position has some logic to not being a Private Variant for Nutter.
My Results Adjusted by BAMsAway
Out of 10 positions I showed Not Tested, 8 of those were tested and found negative. 2 of those positions were actually no reads (or not tested). Those two Positions corresponded with Nutter’s Private Variants at YFull which were not considered Private Variants by FTDNA. When I check Nutter’s Position 19374424, I see that there were no reads at FTDNA:
I am thankful to David Vance at the L513 Facebook Page who steered me to BAMsAway.
Updating My Brother’s Results
My guess is that my brother’s BigY BAMsAway results should be similar to mine. After some copying and pasting into BAMsAway, I get these results for Jim:
For Position #13669903, BAMsAway confirms that Jim only had one read (but that was a negative for the Variant).
Updating Steve’s Results
FTDNA shows that Steve has 5 Private Variants:
The arrow points to the BAMsAway extension for the FTDNA Chromosome Browser. When I choose the extension a popup asks me to add the new SNP name or position:
When I do that, a new position is added to Steve’s list of Private Variants:
I choose the user added position to get this:
This shows that Steve is clearly negative for this Variant. He has no mutation from ‘T’. Here are Steve’s results:
This gives clarity to show that Steve is negative for other A11134 testers’ Private Variants. He gets a No Read for 19374424. This is apparently in a difficult to read portion of the Y Chromosome.
John N’s Results
So far, my chart is shaping up well. John has four Private Variants.
I gave John N a questionable for 13807922 as he had only 4 reads. However, they were all negative. I would say negative. John N also has no reads for 19374424.
Summary of Steve, John N and Nutter
These are the three who tested postive for A11134, but did not form a branch below that level. My major question is why Nutter does not have a Private Variant at 6906758. I will likely write to FTDNA to ask why. I had previously checked Nutter’s results to make sure that he was negative for the 7 SNPs in my Haplogroup. Those are the 7 SNPs at the end of the list above.
Michael, Lawrence and John R
These three BigY testers are in a separate genealogical group that I call the Quaker Line of Hartleys. The ancestor of this group escaped persecution in Lancashire, England and came to Quaker-friendly Pennsylvania around the year 1700. The genealogy of this group can be traced to some time in the 1600’s.
Because I had added NTs or Not Tested to their list based on their incomplete downloadable files, I would like to correct that information using the BAMsAway extension. That will corrrect my comparison chart of Private Variants.
Lawrence and Position 7153793
One of the first interesting results is for Lawrence in position 7153793:
Lawrence has three positive reads for this position. I could argue that this result should form a new branch of ‘Quaker’ Hartleys. YBrowse has two SNPs for this position, but the first is a G to C mutation where Lawrence has a G to A mutation:
The second SNP is listed twice for some reason, but has the G to A mutation:
My feeling is that Lawrence should be in a new Branch called MF205420. This is also consistant with the genealogy:
John and Lawrence share a branch. However, Michael would have to be negative for this Variant for this to be a true Branch separate from John and Lawrence. Michael had an older test:
His test did not cover that position. That means that it is not clear whether MF205420 would apply to all three testers or just two. So this is a case where there should be an extra SNP, but it is not clear where it belongs.
Here is the end of what I looked up for Lawrence:
I indicated in the notes that Lawrence had 3 positive reads. For 13807922, Lawrence had 2 negative reads which would be expected.
John R’s BAMsAway Results
I have five more NTs to get rid of. There were no surprises with this recent BigY test:
This is what I have so far. It was interesting to look at the results. You don’t know whwat you will find until you look. It would be interesting (but take a little work) to fill in the rest of the blanks.
More on Lawrence
Larwence has 6 Private Variants:
Here I filled in the rest of Lawrence’s blanks including the SNPs from my branch of Hartleys:
Quaker Line Michael
Michael took the older BigY500 test. I had missed one of his Private Variants last time, so I will add that in:
Michael may find more Private Variants if he updates to BigY700.
Michael had 2 negative reads for one of Lawrence’s Private Variants. He also had no reads for two of my Branch’s newer SNPs which makes sense.
John R’s Results Completes the Quaker Hartley Analysis
- Here we see the difference between Michael’s BigY500 test and Lawrence and John R’s BigY700 test. Michael has many more ‘no reads’.
- Where there is more than one B? in a row, my note at the end is ambiguous
- I probably should have had different colors for the B? designation depending on whether the low read was positive or negative.
- Some results are more important than others. For example, the results within the Hartley Quaker Group is more important than comparing the Hartley Quaker Group with the non-Quaker Group as we know that those two are not closely related by genealogy.
Filling In Nutter
I did see one unexpected result here:
Nutter had 7 positive reads for a Private Variant that John R in the Hartley Quaker Group had. I made the notation withing the cell and added that the mutation was G to A. Here is what John R shows:
That means that it looks like John R’s Private Variant is not really Private. That is why it pays to look at each of these positions.
MF205420
This Position describes MF205420 which I mentioned above. Apparently, this could be another Hartley-wide Variant. Now I want to see the results for the other Hartley BigY testers. Here it looks like I have found a new Hartley SNP:
However, to be sure, I need to go upstream one level to Mawdsley:
He has 9 negative reads for this position. What that means is that John R’s Private Variant of 7153793 should actually be SNP MF205420 in the A11134 Hartley Group:
Here I have pointed to where MF205420 should be added. Here John R had at least 10 reads, so the 10 read rule came into play:
I just need to convince FTDNA to add MF205420 to the Hartley Group. MF is apparently the designation for a Chinese Company. So far, it has paid off to look at all these positions.
Filling in John N’s Blanks
I don’t see any surprises here:
Filling in Steve’s Blanks
No surprises here.
Joel and Jim
Any difference between these two brothers should be from testing coverage.
It doesn’t look like a lot, but it took a while to get all this information. The two recommendations are noted in yellow in the Note Column. The yellow BY is the same as the Y for the last 7 SNPs in the list. The BNR is equivalent to what I thought I was getting in my previous list where I had NT for Not Tested.
Summary and Conclusions
- I had tried to do an analysis of A11134 BigY testers using downloadable files. However, the results were confusing and I found out that these files are not complete.
- I used BAMsAway and found the complete picture
- From my analysis, Nutter needs one more Private Variant than he has.
- Also, the A1134 should have one more SNP in it’s group for a total of three SNPs. The new SNP would be MF205420. That SNP is now a Private SNP that John R has from the Quaker Hartley group. However, 5 other testers who had reads all had positive reads for that SNP (though below what FTDNA usually finds adequate).