Y Haplogroup prediction help

[ArmandoR1b]

Thanking everyone for their responses here,
I don't think I am L21 positive, my 23andme browser gave me ancestral, not derived, for that marker, and it didn't define my haplogroup further than the generic r1b1b2a1a IIRC... I also did a 5$ promethease test in which the highest marker I got was the P311 (rs9785659). If I'm correct, this also means it's just undefined.

If 23andme gave you r1b1b2a1a then you are definitely negative for U106, L21, and U152. I have never seen a person get a false negative for those SNPs at 23andme. The only additional SNPs almost directly downstream from P312 tested by AncestryDNA v2 are DF19 and L238.

These are the SNPs tested by 23andme v4 (except for P312)

R1b1b2 rs9786153 T->C R1b-M269
R1b1b2a rs9786142 T->A R1b-L49
R1b1b2a1 rs9786140 G->A R1b-L51
R1b1b2a1a rs13304168 C->T L52 (phylogenetically equivalent to L11/S127, L151, P310/S129, P311/S128
R1b1b2a1a1 rs16981293 C>T (M405/S21/U106) R1b-U106
R1b1b2a1a1a rs17222279 G->A (M467/S29/U198) downstream of R1b-U106
R1b1b2a1a1d rs13303755 G->T (L48) downstream of R1b-U106
R1b1b2a1a1d1 rs34283263 G->A (L47) downstream of R1b-U106
R1b1b2a1a1d1a rs34738655 G->A L44
R1b1b2a1a1d1a1 rs35760092 T->G L45, L46, L164
R1b1b2a1a2 rs34276300 C->A (P312) not tested in v3 or v4
R1b1b2a1a2b i3000029 A->T M153 downstream of DF27
R1b1b2a1a2c i3000043 G->A M167/SRY2627 downstream of DF27
R1b1b2a1a2d rs1236440 C->T (S28) R1b-U152 downstream of P312
R1b1b2a1a2d3* rs2566671 C->T R1b-L2 downstream of R1b-U152
R1b1b2a1a2d3a rs7067305 G->A R1b-L20 downstream of R1b-L2
R1b1b2a1a2f rs11799226 C->G (L21) R1b-L21 downstream of P312
R1b1b2a1a2f2 rs20321 G->A R1b-M222 downstream of R1b-L21

While I'm at it, this was also found on the promethease report

" gs262 R1b1a2a1a subclades with hotspots around Normandy, and Milan R1b1a2a1a also known as P312, based on the limited information available with an Ancestry.com test Subclades such as L21 or U152 are also possible *L21 http://www.eupedia.com/images/conten...up-R1b-L21.gif *U152 http://www.eupedia.com/images/conten...up-R1b-S28.gif http://boards.ancestry.com/topics.dnaresearch.generalresearch/772.2.1.1.1.1.1.1.3.1.1.1.1/mb.ashx"

I don't know if this is found on all of them or if it's specific to mine.

P312 is not tested by AncestryDNA or by 23andme unless you had the 23andme v2 test. Your 23andme result already shows that you are negative for both L21 and U152 so it looks like Promethease hasn't updated it's analysis. Was the Promethease report from an AncestryDNA or a 23andme file?

Screenshot of the Morley Report.. unsure if this is what is needed. This was using the AncestryDNA results, the 23andme results were the same except the first prediction was R1b1a2a1a R1b-L11 (R1b-L151, R1b-YSC0000082).

Attachment 12209

I actually need the bottom part of that. Go to the same page then scroll down on the right until you get to the bottom. Then get that screenshot and post it.

Have you had any STR testing with FTDNA or Yseq?

[sktibo]

Promethease report was ancestry DNA. my 23andme is v3, fwiw. No y testing with ftdna or any other, only 23.
I'll get the bottom part of the Morley report posted later today. Thank you again for your help

[sktibo]

Attachment 12222

Bottom of the morley report

[ArmandoR1b]

Attachment 12222

Bottom of the morley report

You can see from that report that you are negative for L21 because it is in a red box. That is also in agreement with your 23andme result. Under normal circumstances anything downstream from L21 should automatically be considered negative unless you are positive for a lot of SNPs between L21 and R1b-PF825.

Also notice that L430 is not in a green box so the program did not report a positive for that SNP so there was never a reason to mention that SNP. R1b-PF825 is in a green box but since there are two mutations at that same position one being PF825.1 G>A which is for haplogroup A0~ and the other PF825.2 for haplogroup R1b but that is also G>A and both of them are at position 17054132.

I finally found the problem though. I had to run another kit through the same process that you did but in Step Three: Download Felix Immanuel's 23andMe to Y-SNP Converter I chose SAVE DISPLAYED TABLE instead of Save Y-SNPs

Then I looked for position 17054132 and it shows M9194/PF825 Yes rs567410971 Y 17054132 G

When I look up M9194 at Ybrowse and at ISOGG it is also G>A

The displayed table and the AncestryDNA v2 raw file both show a result of G.

Felix Immanuel's 23andMe to Y-SNP Converter gave you a false positive for R1b-PF825.

Now if you want to find your subclade you should get the YSEQ R1b Orientation Panel or the LivingDNA test, The Yseq.net is cheaper and faster though. You are mostly likely positive for DF27.

[sktibo]

You can see from that report that you are negative for L21 because it is in a red box. That is also in agreement with your 23andme result. Under normal circumstances anything downstream from L21 should automatically be considered negative unless you are positive for a lot of SNPs between L21 and R1b-PF825.

Also notice that L430 is not in a green box so the program did not report a positive for that SNP so there was never a reason to mention that SNP. R1b-PF825 is in a green box but since there are two mutations at that same position one being PF825.1 G>A which is for haplogroup A0~ and the other PF825.2 for haplogroup R1b but that is also G>A and both of them are at position 17054132.

I finally found the problem though. I had to run another kit through the same process that you did but in Step Three: Download Felix Immanuel's 23andMe to Y-SNP Converter I chose SAVE DISPLAYED TABLE instead of Save Y-SNPs

Then I looked for position 17054132 and it shows M9194/PF825 Yes rs567410971 Y 17054132 G

When I look up M9194 at Ybrowse and at ISOGG it is also G>A

The displayed table and the AncestryDNA v2 raw file both show a result of G.

Felix Immanuel's 23andMe to Y-SNP Converter gave you a false positive for R1b-PF825.

Now if you want to find your subclade you should get the YSEQ R1b Orientation Panel or the LivingDNA test, The Yseq.net is cheaper and faster though. You are mostly likely positive for DF27.

Interesting! Thank you for all your help with this. I don't think I'll order from Yseq because at the moment I'm eagerly awaiting the arrival of my living DNA kit and hopefully It'll show me my Y haplogroup. DF 27 is what I would expect as my most distant paternal ancestor is from the Ile de Re, France. Previously I thought that I might be U-106 because my surname has a possible Visigothic origin, but I suppose that's not likely to be the case. You're a wealth of knowledge on this stuff Armando, and I thank you again for your help in this matter.

[ArmandoR1b]

Interesting! Thank you for all your help with this. I don't think I'll order from Yseq because at the moment I'm eagerly awaiting the arrival of my living DNA kit and hopefully It'll show me my Y haplogroup. DF 27 is what I would expect as my most distant paternal ancestor is from the Ile de Re, France. Previously I thought that I might be U-106 because my surname has a possible Visigothic origin, but I suppose that's not likely to be the case. You're a wealth of knowledge on this stuff Armando, and I thank you again for your help in this matter.

Just something to keep in mind if LivingDNA gives you a result of P312. I doubt they are going to test DF27 accurately but no doubt that they will accurately test a lot of SNPs downstream from DF27. The problem is that you can be negative for all of the SNPs downstream from DF27 tested by LivingDNA. It would be at that point that you would want to order a DF27 test from Yseq.

[razyn]

I must admit that this topic has been, and probably will continue to be, below my radar most of the time. It has cropped up in recent conversations on DF27, and more specifically DF17, topics; so I looked into it just a bit. Particularly in the case of the NevGen Predictor. I think this page has not been cited yet: http://www.nevgen.org/AboutNevGen.html

It is lengthy, detailed, and informative. There have been several updates to the predictor, and the most recent ones are summarized more or less as they occur, at the bottom of the above-linked web page. If you want to catch up on glitches found, and improvements made, since this (Anthrogenica) thread was last updated, scroll to the bottom and read the more recent entries that discuss any haplogroup that might interest you.

[ArmandoR1b]

I must admit that this topic has been, and probably will continue to be, below my radar most of the time. It has cropped up in recent conversations on DF27, and more specifically DF17, topics; so I looked into it just a bit. Particularly in the case of the NevGen Predictor. I think this page has not been cited yet: http://www.nevgen.org/AboutNevGen.html

It is lengthy, detailed, and informative. There have been several updates to the predictor, and the most recent ones are summarized more or less as they occur, at the bottom of the above-linked web page. If you want to catch up on glitches found, and improvements made, since this (Anthrogenica) thread was last updated, scroll to the bottom and read the more recent entries that discuss any haplogroup that might interest you.

I have tried the updated version of Nevgen in the past few weeks with more than a dozen kits that have already had SNP testing, some with 67 markers and some with 37 markers, and there are still a lot of them that they don't predict accurately. I have found that it's only some deep subclades that are fairly accurate.

[vettor]

If 23andme gave you r1b1b2a1a then you are definitely negative for U106, L21, and U152. I have never seen a person get a false negative for those SNPs at 23andme. The only additional SNPs almost directly downstream from P312 tested by AncestryDNA v2 are DF19 and L238.

These are the SNPs tested by 23andme v4 (except for P312)

R1b1b2 rs9786153 T->C R1b-M269
R1b1b2a rs9786142 T->A R1b-L49
R1b1b2a1 rs9786140 G->A R1b-L51
R1b1b2a1a rs13304168 C->T L52 (phylogenetically equivalent to L11/S127, L151, P310/S129, P311/S128
R1b1b2a1a1 rs16981293 C>T (M405/S21/U106) R1b-U106
R1b1b2a1a1a rs17222279 G->A (M467/S29/U198) downstream of R1b-U106
R1b1b2a1a1d rs13303755 G->T (L48) downstream of R1b-U106
R1b1b2a1a1d1 rs34283263 G->A (L47) downstream of R1b-U106
R1b1b2a1a1d1a rs34738655 G->A L44
R1b1b2a1a1d1a1 rs35760092 T->G L45, L46, L164
R1b1b2a1a2 rs34276300 C->A (P312) not tested in v3 or v4
R1b1b2a1a2b i3000029 A->T M153 downstream of DF27
R1b1b2a1a2c i3000043 G->A M167/SRY2627 downstream of DF27
R1b1b2a1a2d rs1236440 C->T (S28) R1b-U152 downstream of P312
R1b1b2a1a2d3* rs2566671 C->T R1b-L2 downstream of R1b-U152
R1b1b2a1a2d3a rs7067305 G->A R1b-L20 downstream of R1b-L2
R1b1b2a1a2f rs11799226 C->G (L21) R1b-L21 downstream of P312
R1b1b2a1a2f2 rs20321 G->A R1b-M222 downstream of R1b-L21



P312 is not tested by AncestryDNA or by 23andme unless you had the 23andme v2 test. Your 23andme result already shows that you are negative for both L21 and U152 so it looks like Promethease hasn't updated it's analysis. Was the Promethease report from an AncestryDNA or a 23andme file?




I actually need the bottom part of that. Go to the same page then scroll down on the right until you get to the bottom. Then get that screenshot and post it.

Have you had any STR testing with FTDNA or Yseq?

On a side note...23andme in DNA matchings has the first five people ( after family ) who match my father are noted as ydna of
R1b1b2a1a1d1a rs34738655 G->A L44 ............

Does this indicate anything in regards to relations outside of my fathers ydna of T-L131 and mtdna of T2b ?

[ArmandoR1b]

On a side note...23andme in DNA matchings has the first five people ( after family ) who match my father are noted as ydna of
R1b1b2a1a1d1a rs34738655 G->A L44 ............

Does this indicate anything in regards to relations outside of my fathers ydna of T-L131 and mtdna of T2b ?

Just that if they are also positive for upstream SNPs then they are positive for that subclade.