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<\/a><\/p>\nMy 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:<\/p>\n
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:<\/p>\n 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:<\/p>\n 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.<\/p>\n 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:<\/p>\n Here is what Nutter’s results show:<\/p>\n 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.<\/p>\n Here is the first Variant that I looked up with no reads found:<\/p>\n Here is how the Browser displays:<\/p>\n 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:<\/p>\n <\/p>\n 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:<\/p>\n 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.<\/p>\n 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:<\/p>\n I am thankful to David Vance at the L513 Facebook Page who steered me to BAMsAway.<\/p>\n 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:<\/p>\n For Position #13669903, BAMsAway confirms that Jim only had one read (but that was a negative for the Variant).<\/p>\n FTDNA shows that Steve has 5 Private Variants:<\/p>\n 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:<\/p>\n When I do that, a new position is added to Steve’s list of Private Variants:<\/p>\n I choose the user added position to get this:<\/p>\n This shows that Steve is clearly negative for this Variant. He has no mutation from ‘T’. Here are Steve’s results:<\/p>\n 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.<\/p>\n So far, my chart is shaping up well. John has four Private Variants.<\/p>\n 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.<\/p>\n 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.<\/p>\n 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.<\/p>\n 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.<\/p>\n One of the first interesting results is for Lawrence in position 7153793:<\/p>\n 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:<\/p>\n The second SNP is listed twice for some reason, but has the G to A mutation:<\/p>\n My feeling is that Lawrence should be in a new Branch called MF205420. This is also consistant with the genealogy:<\/p>\n 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:<\/p>\n 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.<\/p>\n Here is the end of what I looked up for Lawrence:<\/p>\n I indicated in the notes that Lawrence had 3 positive reads. For 13807922, Lawrence had 2 negative reads which would be expected.<\/p>\n I have five more NTs to get rid of. There were no surprises with this recent BigY test:<\/p>\n 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.<\/p>\n Larwence has 6 Private Variants:<\/p>\n Here I filled in the rest of Lawrence’s blanks including the SNPs from my branch of Hartleys:<\/p>\n <\/p>\n <\/p>\n Michael took the older BigY500 test. I had missed one of his Private Variants last time, so I will add that in:<\/p>\n Michael may find more Private Variants if he updates to BigY700.<\/p>\n 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.<\/p>\n I did see one unexpected result here:<\/p>\n 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:<\/p>\n 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.<\/p>\n 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:<\/p>\n However, to be sure, I need to go upstream one level to Mawdsley:<\/p>\n 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:<\/p>\n 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:<\/p>\n 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.<\/p>\n I don’t see any surprises here:<\/p>\n No surprises here.<\/p>\n Any difference between these two brothers should be from testing coverage.<\/p>\n<\/a><\/p>\nBAMsAway<\/h2>\n
<\/a><\/p>\n<\/a><\/p>\n6906758<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nBAMsAway ‘No Reads Found’ at 13807922<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\nMy Results Adjusted by BAMsAway<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nUpdating My Brother’s Results<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nUpdating Steve’s Results<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\nJohn N’s Results<\/h3>\n
<\/a><\/p>\nSummary of Steve, John N and Nutter<\/h3>\n
Michael, Lawrence and John R<\/h3>\n
Lawrence and Position 7153793<\/h4>\n
<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\nJohn R’s BAMsAway Results<\/h4>\n
<\/a><\/p>\nMore on Lawrence<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nQuaker Line Michael<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nJohn R’s Results Completes the Quaker Hartley Analysis<\/h2>\n
<\/a><\/p>\n\n
Filling In Nutter<\/h3>\n
<\/a><\/p>\n<\/a><\/p>\nMF205420<\/h4>\n
<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\n<\/a><\/p>\nFilling in John N’s Blanks<\/h3>\n
<\/a><\/p>\nFilling in Steve’s Blanks<\/h3>\n
<\/a><\/p>\nJoel and Jim<\/h3>\n