My Y-DNA results vs. distant paternal relatives

[plans]

NatGeo Geno2.0 gave me G-P303. I wasn't sure if that was as specific as they went or if I was baseline P303, so I did the FTDNA Y-DNA test. It gave me "presumed" G-M201 and I found I had to buy SNPs to narrow it down. They offered a pretty-much-everything-G pack, "G - M201v2 SNP Pack," so I bought it. I just got the results, which say G-P303 "tested positive", but "tested negative" or "presumed negative" for everything below it.

Here's the thing. One of my matches on FTDNA Y-DNA tested his down to G-Z6147. He lists his earliest known paternal ancestor as someone who appears to be my fifth great grandfather's brother, so we presumably share their father as our most recent common ancestor. Someone I found through a genealogy site who is descended from the same fifth great grandfather as I has his tested down to G-Z6885. Z6147 is downstream of that, so I assumed I would get Z6147, since these groups are thousands of years old, and my lineage diverged from these fellows only a few hundred years ago. For me, both of those subgroups have an asterisk and "No call or heterozygous call."

Am I correct in assuming that my Y-haplogroup is G-Z6147 and that my chromosome just happens to have a mutation that masks that fact?

[spruithean]

Did the SNP pack you ordered from FTDNA test for anything below P303?

[plans]

It tested a great deal of them. L140 and most of its subgroups were tested and are red "Tested Negative" for me. The rest of the subgroups for it are black "Presumed Negative" because since I don't have the big ones, I probably don't have the downstreams. L140 is supposed to be the most common G subgroup, especially in Europe. BY28175, which is a sister to L140, is one of only two that are still blue for me, which means they weren't tested and can't be Presumed Positive/Negative because there's a downstream that is No Call. The subgroups of it for me are as follows:

BY28175 > M278 (red)
BY28175 > Z6885 (no call) > Z39310 (red) > Z39308 (red)
BY28175 > Z6885 (no call) > Z6363 (blue) > Z6147 (no call)
BY28175 > Z30503 (red) > Z30520 (black) > (there are several layers of groups here that are mostly black with some red)

As you can see, Z6885 and Z6147 can't be called, and they're the only types I've seen in my matches. I'm assuming this means it's my group, but that they can't make a 100% determination for some reason. I'm wondering if anyone else got similar results, where they can't be placed in a group with relatives, recent or distant, because of No Call.

[spruithean]

Perhaps you should test those Z6147/Z6885 and related SNPs? It's possible they couldn't get a good enough read due to various reasons. I think YSEQ may have some panels related to those SNPs that are for a very reasonable price.

[td120]

Both snips are $18 each at Yseq and they're fast.
For some reason FTDNA could not read them properly I guess.
Many times doing a full sequence proves to be the way to go. $395 at FGC (YElite) and roughly the same price at FTDNA (BigY-700) when on sale.
This should be what was in the SNP pack (some snips are added or removed at FT discretion).
http://miroise.org/GparADN/g-m201v2-snp-pack-119/

[Regio X]

Am I correct in assuming that my Y-haplogroup is G-Z6147

Yes. Considering that you and that G-Z6147 guy are closely related in male line, and the fact you tested P303+ L140- (somewhat uncommon) is an evidence of relationship specifically in this context, then we can assume you're also G-Z6147.

https://www.yfull.com/tree/G-Z6885/

and that my chromosome just happens to have a mutation that masks that fact?

Not sure what you meant, but the no call or heterozygous call doesn't have to do with a mutation "masking" the result. You must have an Adenine at the correspondant position, which could not be read properly, for some reason.

https://ybrowse.org/gb2/gbrowse_deta...ature_id=45274

Btw, if you tested in FTDNA, you can joing the G-Root Project and clarify your doubts there.

[plans]

Thank you, Regio X. That's what I was looking for.

I just don't know what "no call or heterozygous call" actually means, or what causes it, besides the fact that they can't positively say yes or no. Would a no call result be due to one's DNA in general or just the specific sample they used? Could taking the test again with a new sample give a positive result, or is that just how all of my DNA results would be? Would using another service like Yseq, as others suggested, provide a different result, or would it likely result in a no call as well? Would a close male relative, like a brother, produce the same no call?

I'm confident now that I am G-Z6147, but having it confirmed by FTDNA after paying for the SNP pack would have been nice.

[Regio X]

Thank you, Regio X. That's what I was looking for.

I just don't know what "no call or heterozygous call" actually means, or what causes it, besides the fact that they can't positively say yes or no. Would a no call result be due to one's DNA in general or just the specific sample they used? Could taking the test again with a new sample give a positive result, or is that just how all of my DNA results would be? Would using another service like Yseq, as others suggested, provide a different result, or would it likely result in a no call as well? Would a close male relative, like a brother, produce the same no call?

I'm confident now that I am G-Z6147, but having it confirmed by FTDNA after paying for the SNP pack would have been nice.

Hi. I got a technical answer about SNP Packs few time ago which may be useful for you. Here it is, adapted by myself.

Some SNPs are not ideal for specific Panels in specific sequencing platforms.
SNP Packs are sequenced on a platform that demands primers to be designed in such a way as to fit into a molecular weight scale with many other SNPs in the same Panel.
Being so, sometimes certain SNPs simply do not fit in very well. Often times it's due to the region in which a SNP resides, but not always.
That said, the primary consideration for SNPs to be included in the tree is phylogenetic consistency. SNPs and/or branching points are not eliminated simply because they are tricky or impossible to sequence on a given platform.

I noticed that certain SNPs, in certain Packs, tend to be problematic, for technical reasons, so it's not necessarily a matter of the quality of the sample. Z6147 is especially problematic in the SNP Pack you mentioned, and I bet no-calls are the rule. Z6885 is a bit better, but also with no-calls occasionally.
A call demands a certain number of reads, and a certain proportion of homozygous. In BigYs, for example, afaik FTDNA requires 10 reads to make a call, and in the old BigY there were some important sites not "enriched" to encourage reads. Without this enrichment, often the site just occasionally got some few reads. BigY700 has a better coverage in comparison, and there are tests which cover virtually the entire Y chromosome.

An ambiguous call, or spurious heterozygous genotyping call, may be consequence of stray misaligned reads - not rare -, because the related region is similar/identical to other regions in any chromosome (including Y itself). They're generally in specific parts of the chromosome, but let's leave the details aside.

Answering you more directly:

Would a no call result be due to one's DNA in general or just the specific sample they used?

Not to the DNA, and not necessarily to the sample.

Could taking the test again with a new sample give a positive result, or is that just how all of my DNA results would be?

Would a close male relative, like a brother, produce the same no call?

Sometimes, yes, but wait. Considering specifically the Z6147 and this specific Panel, there would be a very high chance of getting the same no-call, with your sample or any other (brother's, mine or whoever)

Would using another service like Yseq, as others suggested, provide a different result, or would it likely result in a no call as well?

Very likely a different result, and a positive/negative one. YSEQ uses Sanger sequencing, so no worries. In fact, they use it even as a way to verify certain mutations obtained by a NGS test. If you do wanna confirm you're Z6147+, go ahead with YSEQ, a cheap option.

[torzio]

Hi. I got a technical answer about SNP Packs few time ago which may be useful for you. Here it is, adapted by myself.



I noticed that certain SNPs, in certain Packs, tend to be problematic, for technical reasons, so it's not necessarily a matter of the quality of the sample. Z6147 is especially problematic in the SNP Pack you mentioned, and I bet no-calls are the rule. Z6885 is a bit better, but also with no-calls occasionally.
A call demands a certain number of reads, and a certain proportion of homozygous. In BigYs, for example, afaik FTDNA requires 10 reads to make a call, and in the old BigY there were some important sites not "enriched" to encourage reads. Without this enrichment, often the site just occasionally got some few reads. BigY700 has a better coverage in comparison, and there are tests which cover virtually the entire Y chromosome.

An ambiguous call, or spurious heterozygous genotyping call, may be consequence of stray misaligned reads - not rare -, because the related region is similar/identical to other regions in any chromosome (including Y itself). They're generally in specific parts of the chromosome, but let's leave the details aside.

Answering you more directly:

Not to the DNA, and not necessarily to the sample.


Sometimes, yes, but wait. Considering specifically the Z6147 and this specific Panel, there would be a very high chance of getting the same no-call, with your sample or any other (brother's, mine or whoever)

Very likely a different result, and a positive/negative one. YSEQ uses Sanger sequencing, so no worries. In fact, they use it even as a way to verify certain mutations obtained by a NGS test. If you do wanna confirm you're Z6147+, go ahead with YSEQ, a cheap option.

yfull does 80 reads ..............maybe , its one reason their tree keeps getting monthly version updates

[Regio X]

yfull does 80 reads ..............maybe , its one reason their tree keeps getting monthly version updates

Not sure what you mean. YFull does interpretations, and works with third party BAM files. In fact, it considers SNPs with three reads or more.

[plans]

I did the YSEQ test for Z6147 and it's showing the result A+. I'm a little unclear, but it looks like the plus sign means that I have that mutation. Apparently the ancestral marker is T and the mutation is A. There's a bunch of other tests on there they did for free and they all have minus signs.

[Regio X]

I did the YSEQ test for Z6147 and it's showing the result A+. I'm a little unclear, but it looks like the plus sign means that I have that mutation. Apparently the ancestral marker is T and the mutation is A. There's a bunch of other tests on there they did for free and they all have minus signs.

You don't even need to bother checking the associated mutation. In YSEQ, "+" means positive, and that's it.
You're positive for Z6147.

[plans]

Thank you for all the help and the recommendation.