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Afshar
09-24-2015, 02:04 PM
A big whole bunch of them. Some have less than ten reads which I find unreliable. But there are also some interesting snps, with a decent coverage >100x, which seem to belong to another haplogroup. Is it that these SNPs are not investigated enough yet, and incorrectly assigned to some haplogroup, or do these notsofalse snps mean anything.

Afshar
09-24-2015, 02:13 PM
Or are these related to mapping issues

Cofgene
09-24-2015, 04:30 PM
A big whole bunch of them. Some have less than ten reads which I find unreliable. But there are also some interesting snps, with a decent coverage >100x, which seem to belong to another haplogroup. Is it that these SNPs are not investigated enough yet, and incorrectly assigned to some haplogroup, or do these notsofalse snps mean anything.

Some are assembly errors and some come from heterogeneous regions. For assembly errors you can take the time to extract the reads out of the BAM file and rerun the assembly and SNP analysis with a different set of parameters. You might clears up some small sections and get a better feel for some of the notsofalse SNPs. In terms of SNPs from other haplogroups showing up. If they are directly upstream of you then they would be expected to be present. If they are not then look at whether you have a .x recurrent showing up in your line/branch. SNPs can and will show up across multiple haplogroups. No big deal. To clear up the fuzzy sections the next step would be to see if there are some Sanger primers in the section and order some of those from YSEQ.NET to check out if some of those notsofalse SNPs are real. Finally just wait until the next step in sequencing arrives where you can get longer read lengths. Longer lengths will clear up the question about what SNPs are present in most of these questionable regions.

Afshar
09-24-2015, 04:56 PM
Some are assembly errors and some come from heterogeneous regions. For assembly errors you can take the time to extract the reads out of the BAM file and rerun the assembly and SNP analysis with a different set of parameters. You might clears up some small sections and get a better feel for some of the notsofalse SNPs. In terms of SNPs from other haplogroups showing up. If they are directly upstream of you then they would be expected to be present. If they are not then look at whether you have a .x recurrent showing up in your line/branch. SNPs can and will show up across multiple haplogroups. No big deal. To clear up the fuzzy sections the next step would be to see if there are some Sanger primers in the section and order some of those from YSEQ.NET to check out if some of those notsofalse SNPs are real. Finally just wait until the next step in sequencing arrives where you can get longer read lengths. Longer lengths will clear up the question about what SNPs are present in most of these questionable regions.
I thought so, because they belong to a wide array of haplogroups. Your approach is good, my funds are not haha.

crossover
09-24-2015, 06:51 PM
Some are assembly errors and some come from heterogeneous regions. For assembly errors you can take the time to extract the reads out of the BAM file and rerun the assembly and SNP analysis with a different set of parameters. You might clears up some small sections and get a better feel for some of the notsofalse SNPs. In terms of SNPs from other haplogroups showing up. If they are directly upstream of you then they would be expected to be present. If they are not then look at whether you have a .x recurrent showing up in your line/branch. SNPs can and will show up across multiple haplogroups. No big deal. To clear up the fuzzy sections the next step would be to see if there are some Sanger primers in the section and order some of those from YSEQ.NET to check out if some of those notsofalse SNPs are real. Finally just wait until the next step in sequencing arrives where you can get longer read lengths. Longer lengths will clear up the question about what SNPs are present in most of these questionable regions.

well that explains why while promethease predicted my grandpa's haplogroup to be r, he tested postive for a j and an i snp.

ArmandoR1b
09-24-2015, 07:27 PM
well that explains why while promethease predicted my grandpa's haplogroup to be r, he tested postive for a j and an i snp.

Not at all. YFull analyzes NGS (Next Generation Testing) results. They never confuse haplogroups. There is only a relatively small number of ambiguous SNPs in the thousands that they analyze.

Promethease doesn't analyze NGS test results. It only analyzes the results of files from FTDNA Family Finder, AncestryDNA, and 23andme. AncestryDNA tests an extremely limited portion of the Y chromosome. Family Finder doesn't test it at all. 23andme does limited testing of the Y-chromosome but enough to tell which haplogroup and major subclade a person belongs to. It never confused R, J and I. Your grandfather's ambiguous are because you haven't purchased a Y-DNA test for him from FTDNA, Yseq, or FGC or a 23andme test.

Afshar
09-24-2015, 07:40 PM
What immediately caught my eye was the series of l373-l379 that seem positive, which apparently belong to haplo G.
I think most of these snps are unreliable

ArmandoR1b
09-24-2015, 08:33 PM
What immediately caught my eye was the series of l373-l379 that seem positive, which apparently belong to haplo G.
I think most of these snps are unreliable

L373 was found in hg G-L14 and J-L70 WTY participants http://bit.ly/1OwV6p7 which was done by FTDNA. I am sure the SNP is reliable but highly recurrent so just as long as someone has enough SNPs that are upstream, and in most cases downstream, then the SNP can be properly placed within the haplogroup and subclade that the other positive SNPs are in.

Afshar
09-24-2015, 08:42 PM
We need more testing, thats for sure:)

crossover
09-24-2015, 11:43 PM
Not at all. YFull analyzes NGS (Next Generation Testing) results. They never confuse haplogroups. There is only a relatively small number of ambiguous SNPs in the thousands that they analyze.

Promethease doesn't analyze NGS test results. It only analyzes the results of files from FTDNA Family Finder, AncestryDNA, and 23andme. AncestryDNA tests an extremely limited portion of the Y chromosome. Family Finder doesn't test it at all. 23andme does limited testing of the Y-chromosome but enough to tell which haplogroup and major subclade a person belongs to. It never confused R, J and I. Your grandfather's ambiguous are because you haven't purchased a Y-DNA test for him from FTDNA, Yseq, or FGC or a 23andme test.

apparently the y-snp's ancestry tested were enough for promethease to predict my grandpa's y-dna haplogroup as being r1b1a2a1a1. if he's not r1b1a2a1a1, he's most likely within r1b.

ArmandoR1b
09-25-2015, 02:28 AM
apparently the y-snp's ancestry tested were enough for promethease to predict my grandpa's y-dna haplogroup as being r1b1a2a1a1. if he's not r1b1a2a1a1, he's most likely within r1b.

Maybe, but it's not because of what Cofgene posted and you had quoted. If you want trustworthy results you need to get him a Y-DNA test elsewhere. Additionally, AncestryDNA wasn't good enough to tell you if your grandfather is negative for P312 and if so if he is L21, P312 or U152. L11 is so old it doesn't tell you much without knowing about the other SNPs.

crossover
09-25-2015, 03:00 AM
Maybe, but it's not because of what Cofgene posted and you had quoted. If you want trustworthy results you need to get him a Y-DNA test elsewhere. Additionally, AncestryDNA wasn't good enough to tell you if your grandfather is negative for P312 and if so if he is L21, P312 or U152. L11 is so old it doesn't tell you much without knowing about the other SNPs.

after l11 he tested postive for p310,p311, and m405.

VinceT
09-25-2015, 09:35 AM
after l11 he tested postive for p310,p311, and m405.

M405 = U106 = S21. If your grandfather has a STR haplotype from FTDNA, please join him the R1b-U106 Project at https://www.familytreedna.com/groups/u106/about.

If not, you can pursue further testing for him at YSEQ:
YSEQ-Alpha-Beta: a double panel of 37 STR markers equivalent with FTDNA's YSTR-37 test. [link (http://www.yseq.net/product_info.php?cPath=22_23&products_id=34)]


Find out if he is in haplogroup R-L48. Does promethease or Ancestry report L48 as negative? If not, order L48 at YSEQ. [link (http://www.yseq.net/product_info.php?products_id=97)]

If he is positive for L48, order the R1b-U106-L48 Panel at YSEQ. [link (http://www.yseq.net/product_info.php?cPath=25&products_id=16589)]

If he is negative for L48, order the R1b-U106(xL48) Panel at YSEQ. [link (http://www.yseq.net/product_info.php?cPath=25&products_id=18643)]

Note that YSEQ adds a $5.00 shipping charge on all orders by default, so once the initial test has been performed, use the coupon code IDONTNEEDAKIT to get a $5.00 deduction on all consecutive orders.

ArmandoR1b
09-25-2015, 12:58 PM
after l11 he tested postive for p310,p311, and m405.

Congratulations. Dr. Doug McDonald had reported that U106 shows up in AncestryDNA. The R1b SNPs P312, L21, U152, and of course DF27 don't show up in AncestryDNA files. I double checked my own to verify that. More than 80% of Hispanics that are R1b are P312 but with AncestryDNA they have no way of knowing if they are positive for it and one of the subclades using AncestryDNA's file. Only about 5% are U106 which is more commonly a Germanic SNP.

I hope you follow VinceT's advice. L48 is rs13303755. I'm not seeing a result for it in my file even though I do see rs16981293(C;C) which is U106 in my file.

Another way to cross reference the SNPs is the ISOGG SNP Index using the page at http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

I have to rescind my statements earlier that what is happening at YFull isn't happening with the Promethease report. The SNPs that aren't R1b that show up in your grandfather's report are recurrent and are the same thing that is happening at YFull. The difference is the way the report is provided and how much data the report provides. Here is a YFull sample report - http://www.yfull.com/share/yreport/ad895e00df23dac07378c2e308e1332d/ The recurrent SNPs from other haplogroups won't show up in the report unless they are in the direct line. They will show up in other haplogroups with a search at http://www.yfull.com/search-snp-in-tree/

ArmandoR1b
09-25-2015, 01:04 PM
We need more testing, thats for sure:)

Yes, lots more testing. The important part is to concentrate on the terminal SNPs and phylogenetically equivalent SNPs if the terminal SNP is recurrent in other haplogroups.

crossover
09-25-2015, 04:44 PM
Congratulations. Dr. Doug McDonald had reported that U106 shows up in AncestryDNA. The R1b SNPs P312, L21, U152, and of course DF27 don't show up in AncestryDNA files. I double checked my own to verify that. More than 80% of Hispanics that are R1b are P312 but with AncestryDNA they have no way of knowing if they are positive for it and one of the subclades using AncestryDNA's file. Only about 5% are U106 which is more commonly a Germanic SNP.

I hope you follow VinceT's advice. L48 is rs13303755. I'm not seeing a result for it in my file even though I do see rs16981293(C;C) which is U106 in my file.

Another way to cross reference the SNPs is the ISOGG SNP Index using the page at http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

I have to rescind my statements earlier that what is happening at YFull isn't happening with the Promethease report. The SNPs that aren't R1b that show up in your grandfather's report are recurrent and are the same thing that is happening at YFull. The difference is the way the report is provided and how much data the report provides. Here is a YFull sample report - http://www.yfull.com/share/yreport/ad895e00df23dac07378c2e308e1332d/ The recurrent SNPs from other haplogroups won't show up in the report unless they are in the direct line. They will show up in other haplogroups with a search at http://www.yfull.com/search-snp-in-tree/

yeah i'm considering ordering from yseq since it's cheaper than ftdna. also when i was checking the nueva galicia dna project on ftdna, i saw someone with the same last name as my grandpa with u106+ and l48-. so maybe my grandpa is negative for l48- if he's related to that individual.
i'll probably get the alphabeta first.

VinceT
09-26-2015, 06:14 AM
yeah i'm considering ordering from yseq since it's cheaper than ftdna. also when i was checking the nueva galicia dna project on ftdna, i saw someone with the same last name as my grandpa with u106+ and l48-. so maybe my grandpa is negative for l48- if he's related to that individual.
i'll probably get the alphabeta first.
@crossover, once you get results from YSEQ, please join Group 12 (R1b-U106/M405/S21) so we can evaluate and compare your data with the rest of the project.

ArmandoR1b
09-26-2015, 01:47 PM
yeah i'm considering ordering from yseq since it's cheaper than ftdna. also when i was checking the nueva galicia dna project on ftdna, i saw someone with the same last name as my grandpa with u106+ and l48-. so maybe my grandpa is negative for l48- if he's related to that individual.
i'll probably get the alphabeta first.

I bet that once you are done with STR and SNP testing of your grandfather it will show that he has a common ancestor in the past 500 years with the other person with the same last name.

Since you know that person is negative for L48 he might have a terminal SNP other than U106 in the Haplogroup column. If so, you can search for that SNP at Yseq and test the terminal SNP.