M253 phyloequivalent SNP markers

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Aldon

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Hi

I read an article recently that seemed to imply that to be DF29+ then you have to be positive for all phyloequivalent SNP markers that confirm M253.....is that correct?? The reason I ask is that I have found I am negative for the phyloequivalent SNP marker L64.
 
Aldon said:
Hi

I read an article recently that seemed to imply that to be DF29+ then you have to be positive for all phyloequivalent SNP markers that confirm M253.....is that correct?? The reason I ask is that I have found I am negative for the phyloequivalent SNP marker L64.
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How do you know you’re negative for L64? How many reads did you have for that specific base pair location? What kind of testing did you have done? What does Ftdna have you labeled as? If you truly are negative for one or more phyloequivalent SNPs comprising I1 then that would be very interesting because then a new branch would form on the Haplotree. People that are positive for I-DF29 are also positive for L64 so you would not be positive for I-DF29.

It is possible though that you are simply a “no call” for L64 in which case you could still potentially be positive for DF29.
 
Hi mwauthy, thanks for reply. Tested with 23andme and was designated I-M253. Downloaded raw data to find out more and fed into Morley where I discovered L64 was negative out of 10 phyloequivalents tested by 23andme (found out about phyloequivalent SNP markers on site online). Checked against raw data and was indeed variant C negative instead of T ancestral. Was going to test further with YSEQ I1 panel, now not so sure, which is why I posted this thread.
 
Aldon said:
Hi mwauthy, thanks for reply. Tested with 23andme and was designated I-M253. Downloaded raw data to find out more and fed into Morley where I discovered L64 was negative out of 10 phyloequivalents tested by 23andme (found out about phyloequivalent SNP markers on site online). Checked against raw data and was indeed variant C negative instead of T ancestral. Was going to test further with YSEQ I1 panel, now not so sure, which is why I posted this thread.
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I’m not familiar with the technology 23andMe uses. However, with Ftdna I know that the same base pair location gets many reads and occasionally a negative read will pop up such as 49 T (Thymine) and 2 C (Cytosine). If it clears a certain percentage threshold it’s considered positive or negative. If not it can become an ambiguous “no call.” SNP readings are not always cut and dry especially if the location of the SNP is in an area of the Y chromosome that is difficult to read. I would test with another company such as Ftdna or YSEQ to get some clarity for your questions.
 
Hi mwauthy, thanks, yes I will test with YSEQ and hope they can point me in the right direction downstream.
 
Sorry meant to say I was C ancestral instead of T derived.
 
If you're DF29 you must be positive for all phyloequivalent SNPs of M253. I know with many Big Y test results at FTDNA some SNPs in a pack of related SNPs are labelled brown among green ones to show presumed positive (brown) with positive (green). Either it's due to bad reads, or sample saving procedures that they gloss over certain SNPs.
 
Hi Spruithean 23and me didn't test me for DF29 so I cannot say whether that was positive or negative. However, they did test me for L64 and Morley said that was negative. So I checked the rs-id, which I got from the Isogg tree, for L64 against 23andme raw data....it was negative/ancestral 'C'. This might account for why 23andme and Morley couldn't place me any lower than I-M253, as I'm supposed to be positive for all phyloequivalents of I-M253 to be DF29 or lower. Of course it could be that 23andme's raw data for L64 is wrong. I guess only further testing will decide the issue, so I will take the I1 Superclade Panel with YSEQ soon.
 
Grisdale said:
Hi Spruithean 23and me didn't test me for DF29 so I cannot say whether that was positive or negative. However, they did test me for L64 and Morley said that was negative. So I checked the rs-id, which I got from the Isogg tree, for L64 against 23andme raw data....it was negative/ancestral 'C'. This might account for why 23andme and Morley couldn't place me any lower than I-M253, as I'm supposed to be positive for all phyloequivalents of I-M253 to be DF29 or lower. Of course it could be that 23andme's raw data for L64 is wrong. I guess only further testing will decide the issue, so I will take the I1 Superclade Panel with YSEQ soon.
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Just purchased YSEQ Superclade Panel. Will post results when available
 
Grisdale said:
Just purchased YSEQ Superclade Panel. Will post results when available
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It'll be interesting if you turn out DF29-, perhaps positive for some of the other downstream SNPs of M253, like Z131 (I1b) or Z17925 (I1c).
 
I wouldn't worry too much about this - genotyping on SNP chips can have a few false negatives and positives. I have them myself in these tests - AncestryDNA has false negatives for S107, S108, S111 among the I1 phyloequivalent SNPs. I checked all they SNPs in my 30x WGS and they all read derived (positive) with multiple reads. Also false positives for Z1382 (in haplogroup J1) CTS616 (in haplogroup I2) - both of these turn out as ancestral (negative) with multiple reads when looking at my 30x WGS.
My 23andme test has false positives for Y-SNPs PF3861 (haplogroup I2), L88 (haplogroup J2) - both ancestral (negative) in the WGS.
 
I'd also add that L64 doesn't seem to be a reliable SNP. YFull have given L64 a one-star rating and don't include it among the I1 SNPs on their YFull tree. It's at ChrY position(hg38):10147323 which puts it in the centromere - a region of the Y chromosome that suffers from frequent recombination events.
My own results at that position in the 30x WGS are ambiguous - 1A, 15T, 20C. Most likely L64 is an unreliable SNP.
The Morley predictor uses a tree from 2013 as a reference, so it's a bit out of date.
 
YSEQ won't test L64 - since it's in the centromere, they they will respond with "not recommended" if you ask to test: "Those sections of the Y chromosome suffer from frequent recombination events and are therefore not useful for phylogenetic studies. Unfortunately we can't provide primers for those regions."
 
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