Can someone give me insight to the Revised Reference Cambridge Sequence? I manually posted my DNA results to Ancestry.com and my results indicate I'm an exact match. It appears less than 5% of people tested belong to this group. In layman's terms, what does this mean and how can it assist me genealogy research? My Haplo group is L1b. Thanks, Mike

Nicolas, Thank you for the S series identifications and position correction for S25633 Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Nicolas Taban Sent: Monday, May 26, 2014 1:19 PM To: y-dna-haplogroup-i@rootsweb.com Subject: Re: [yDNAhgI] I-P109 sub tree Ken I saw your update today. Despite I tend to agree that position would be more precise, they are also more difficult to read and remember (a combination of letters and numbers seems easier for the brain). So please note that: 8112824 = S11056 22802502 = S7660 Also, I do not understand why you have 23486236 = S25633 in this place as we are all positive to it. Have you had a look to the slide I sent you (also available on the I1 facebook group)? The main structure of the I-P109 subtree is already there joining both Chromo2 and BigY results (without all the private SNPs). Regards, Nicolas Taban > From: knordtvedt@bresnan.net > To: y-dna-haplogroup-i@rootsweb.com > Date: Fri, 23 May 2014 08:01:49 -0600 > Subject: Re: [yDNAhgI] I-P109 sub tree > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Nicolas Taban > Sent: Friday, May 23, 2014 6:36 AM > To: y-dna-haplogroup-i@rootsweb.com > Subject: [yDNAhgI] I-P109 sub tree > > You seem to exclude position 17819410 that I previously asked to be > seeded. > It regroups (in your slide) "Ca", "R", "Cr" and "A". Have you seeded it > and > concluded that it was not a reliable position? > > [[Yes, indeed it does survive weeding and unites those four. I just missed > it. As is pretty clear, P109 tree is preliminary; it does not include > unique NVs for many individuals yet. KN]] > > > > > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message ------------------------------- To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Y3239 (14888161) Hi Julie, You wrote: “Family Tree DNA did not report any of our 15 Big Y testers as being derived for the novel variant 14888161. However, when the YFull Team analysed the BAMs they identified four L803 men with reads at this position. YFull named the new SNP Y3239.” …. “There are other L803 members in the Project who did not test Big Y that might also benefit if they could test Y3239 (14888161) – however, what would be my chances of requesting FTDNA to add this SNP to their catalogue when it didn’t even get reported for some of these L803s as a Big Y novel variant? I am a bit bewildered by this situation.” Nice job, by the way, correlating your members and on what appears to be a new branch based on the new SNPs you have found. Below, I would like to respond to the bewilderment you expressed. Obviously, what I am saying to you is only my opinion as I do not have any direct one-to-one information from FTDNA or YFull that substantiates the following remarks. Both companies, FTDNA and YFull, are using precisely the same raw data and coverage that is provided in the BAM file to determine any new SNPs. The fact that FTDNA did not report any of your 15 BIG Y testers as being derived for the variant 14888161 is likely be due to the small number of reads obtained (1 to 3). Anything under 55-80 reads at a position is insufficient for the FTDNA filter criteria to call a variant with any level of confidence. Whereas it could be a legitimate SNP and they would miss it by application of their quality filter. It appears that YFull has applied a different algorithm to the same data and has been able to be assured that even given only 3 reads (or even 1) they feel confident that this is a valid SNP. The fact that they chose to name it Y3239 would indicate they are convinced it is not an erroneous base call. As I indicated on this list on April 16 under, “Some Comments on the BIG Y VCF file information” A major limitation of high-throughput DNA sequencing is the high rate of erroneous base calls produced. For instance, Illumina sequencing machines produce errors at a rate of ∼0.1–1 × 10−2 per base sequenced. Erroneous base calls can be largely mitigated by establishing a consensus sequence from high-coverage sequencing reads. FTDNA indicates that the BIG Y coverage is from 55X to 80X, meaning the number of times the Illumina machines read the sequence. Each base read is scored by a quality estimate (reported in the VCF file under QUAL for the alternate allele value) given by Q = -10 Log (p) where p = the error probability for the base. For example if p = 0.01 (1% chance of error) then Q = 20. Quality scores estimate the quality of the consensus sequence. For example at 7X coverage of a particular location we might find a variety of base quality ratings (Q) for the call of either A or G: A(Q35), A (Q45), A(Q40), G(Q4), G(Q12), G(Q12), G(Q6), G(Q8) Which is more likely to be the right call at this position, A or G? In your case the importance of the number of reads criteria to you is that, at risk of missing a valid SNP, FTDNA is choosing to filter out variants that have such few reads (only from 1 to 3 reads) as yours for 14888161, in order to be certain that the ones they do call are in fact legitimate with a high level of confidence. In order to request FTDNA add this SNP to their catalogue when it didn’t even get reported for some of these L803s as a Big Y novel variant, I think you would need to provide convincing evidence that the SNP called by YFull is valid and not an erroneous machine base call. To do that I think the best way to proceed is to have some of your members submit a sample to test that position at Thomas Krahn’s YSEQ company where he uses the (Gold Standard) SANGER method of testing that location. Thomas can advise you whether or not he wishes to test that position based on the 1 to 3 reads produced by BIG Y in the raw data of the BAM file that has been called valid by YFull. If Thomas uses the Sanger method to validate the SNP then you could request FTDNA to add it to the list of SNPs available to test by other members of your group without having to resupply a test sample. You might also want to check with YFull to see what they say as to why they are confident enough to claim a new SNP at that position, and name it, based on only 1 to 3 reads in the high-throughput sequence procedure used by BIGY. How have they determined it is not an erroneous call? I believe that you very likely have indeed found a valid SNP via the YFull analysis and that it is an important branch in your L803 line, so you should pursue it. Hope this helps to at least provide some rationale for the difference between FTDNA not calling a Novel Variant at 14888161 and the findings reported by YFull. Regards, Richard Brewer On Mon, May 26, 2014 at 4:00 AM, Julie Frame Falk <jdf4072@gmail.com> wrote: > Dear Lists > > Many thanks to the YFull team for their wonderful interpretation service. > Some kits have not had processing finalised as yet, but the YFull > Experimental Tree suggests it might be timely for me to post an update for > the I1-L803 sector. Thus far, nine of our 15 Big Y testers are members of > the I1-Z60 project at YFull. > > Herewith a link to a chart showing the new branches downstream of I1-L803 > as determined by the YFull Team: > https://app.box.com/s/w9qhdt8b1hxaas37cqwp > > I have added some notes to the chart to show most distant ancestor > timeframe and geographical locations, but will mention an important point > here as well: > > Family Tree DNA did not report any of our 15 Big Y testers as being > derived for the novel variant 14888161. However, when the YFull Team > analysed the BAMs they identified four L803 men with reads at this > position. YFull named the new SNP Y3239. > > The read details at 14888161 are as follows: > > Kit 181118 / YF01508: 3 reads = 3T: C>T > Kit 150485 / YF01541: 3 reads = 3T: C>T > Kit 136903 / YF01597: 2 reads = 2T: C>T > Kit 84205 / YF01603: 1 read = 1T: C>T > > As can be seen on the chart, and despite the scant number of reads, Y3239 > (14888161) appears to be an important gateway SNP to further branches > downstream. Unfortunately, with the ‘no reads’ at this position, we > cannot determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and > Frame 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is > waiting for a BAM). Has anyone else faced this situation? If so, would > FTDNA likely be open to rechecking these kits at 14888161? I don’t have > any idea of the the Lab process so this may not be feasible, but I sure > would like something definite rather than being left with this ambiguity. > There are other L803 members in the Project who did not test Big Y that > might also benefit if they could test Y3239 (14888161) – however, what > would be my chances of requesting FTDNA to add this SNP to their catalogue > when it didn’t even get reported for some of these L803s as a Big Y novel > variant? I am a bit bewildered by this situation. > > The other branch below L803 is L802 – both of these SNPs discovered in Kit > 64529’s WTY. Now with Big Y we have another branch parallel to L802 > (Y3239) that seems to be taking in many of the L803 families. The > maximum GD between any L803 men is 18 at 111 markers – one L802+ and the > other Y3239+. I highlighted them with red arrows on the chart. > Interestingly, there is only GD 3 between the other L802 and the family of > a Y3238 man – also shown with red arrows. Huge variation. > > Once again, my sincere appreciation to the YFull Team. > > Kind regards > Julie Frame Falk (Admin) > Frame / Freame / Fremault DNA Project > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message

> From: knordtvedt@bresnan.net > To: jdf4072@gmail.com; y-dna-haplogroup-i@rootsweb.com > Date: Mon, 26 May 2014 08:52:28 -0600 > Subject: Re: [yDNAhgI] YFull Interpretation - new branches in I1-L803 > > BigY coverage could be the explanation. BigY does not just measure 10 > million sites in a continuous row. They measure many hundreds, indeed > thousands, of Y segments each hundreds of sites long but separated from the > next segment by a stretch of unread sites. I checked my coverage and > another I have and we both do not cover that site. My coverage starts at > 14888279 and the other fellow's coverage starts at 14888220. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Julie Frame Falk > Sent: Monday, May 26, 2014 5:00 AM > To: I1-Z58andZ63 Project ; Y-DNA Haplogroup I > Subject: [yDNAhgI] YFull Interpretation - new branches in I1-L803 > > Dear Lists > > Many thanks to the YFull team for their wonderful interpretation service. > Some kits have not had processing finalised as yet, but the YFull > Experimental Tree suggests it might be timely for me to post an update for > the I1-L803 sector. Thus far, nine of our 15 Big Y testers are members of > the I1-Z60 project at YFull. > > Herewith a link to a chart showing the new branches downstream of I1-L803 as > determined by the YFull Team: https://app.box.com/s/w9qhdt8b1hxaas37cqwp > > I have added some notes to the chart to show most distant ancestor timeframe > and geographical locations, but will mention an important point here as > well: > > Family Tree DNA did not report any of our 15 Big Y testers as being derived > for the novel variant 14888161. However, when the YFull Team analysed the > BAMs they identified four L803 men with reads at this position. YFull named > the new SNP Y3239. > > The read details at 14888161 are as follows: > > Kit 181118 / YF01508: 3 reads = 3T: C>T > Kit 150485 / YF01541: 3 reads = 3T: C>T > Kit 136903 / YF01597: 2 reads = 2T: C>T > Kit 84205 / YF01603: 1 read = 1T: C>T > > As can be seen on the chart, and despite the scant number of reads, Y3239 > (14888161) appears to be an important gateway SNP to further branches > downstream. Unfortunately, with the ‘no reads’ at this position, we cannot > determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and Frame > 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is waiting for > a BAM). Has anyone else faced this situation? If so, would FTDNA likely be > open to rechecking these kits at 14888161? I don’t have any idea of the > the Lab process so this may not be feasible, but I sure would like something > definite rather than being left with this ambiguity. There are other L803 > members in the Project who did not test Big Y that might also benefit if > they could test Y3239 (14888161) – however, what would be my chances of > requesting FTDNA to add this SNP to their catalogue when it didn’t even get > reported for some of these L803s as a Big Y novel variant? I am a bit > bewildered by this situation. > > The other branch below L803 is L802 – both of these SNPs discovered in Kit > 64529’s WTY. Now with Big Y we have another branch parallel to L802 > (Y3239) that seems to be taking in many of the L803 families. The maximum > GD between any L803 men is 18 at 111 markers – one L802+ and the other > Y3239+. I highlighted them with red arrows on the chart. Interestingly, > there is only GD 3 between the other L802 and the family of a Y3238 man – > also shown with red arrows. Huge variation. > > Once again, my sincere appreciation to the YFull Team. > > Kind regards > Julie Frame Falk (Admin) > Frame / Freame / Fremault DNA Project > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

FWIW, the Full Genomes raw data for my I1-Z138 shows 79/79 reads of C (same as reference) at 14888161. The data looks reliable, although one of the reads says there is an identical sequence on chromosome 4. -----Original Message----- > From: Julie Frame Falk > Sent: Monday, May 26, 2014 5:00 AM > To: I1-Z58andZ63 Project ; Y-DNA Haplogroup I > Subject: [yDNAhgI] YFull Interpretation - new branches in I1-L803 > > Dear Lists > > > > Family Tree DNA did not report any of our 15 Big Y testers as being derived > for the novel variant 14888161. However, when the YFull Team analysed the > BAMs they identified four L803 men with reads at this position. YFull named > the new SNP Y3239. > > The read details at 14888161 are as follows: > > Kit 181118 / YF01508: 3 reads = 3T: C>T > Kit 150485 / YF01541: 3 reads = 3T: C>T > Kit 136903 / YF01597: 2 reads = 2T: C>T > Kit 84205 / YF01603: 1 read = 1T: C>T > > As can be seen on the chart, and despite the scant number of reads, Y3239 > (14888161) appears to be an important gateway SNP to further branches > downstream. Unfortunately, with the ‘no reads’ at this position, we > cannot > determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and Frame > 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is waiting for > a BAM). Has anyone else faced this situation? If so, would FTDNA likely > be > open to rechecking these kits at 14888161? I don’t have any idea of the > the Lab process so this may not be feasible, but I sure would like > something > definite rather than being left with this ambiguity. There are other L803 > members in the Project who did not test Big Y that might also benefit if > they could test Y3239 (14888161) – however, what would be my chances of > requesting FTDNA to add this SNP to their catalogue when it didn’t even get > reported for some of these L803s as a Big Y novel variant? I am a bit > bewildered by this situation. >

Forgot the punch line; you can check the coverage for your L803 people to see first hand if they covered that site for them? Oh, I see, four of the L803 people apparently had coverage there? Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Julie Frame Falk Sent: Monday, May 26, 2014 5:00 AM To: I1-Z58andZ63 Project ; Y-DNA Haplogroup I Subject: [yDNAhgI] YFull Interpretation - new branches in I1-L803 Dear Lists Many thanks to the YFull team for their wonderful interpretation service. Some kits have not had processing finalised as yet, but the YFull Experimental Tree suggests it might be timely for me to post an update for the I1-L803 sector. Thus far, nine of our 15 Big Y testers are members of the I1-Z60 project at YFull. Herewith a link to a chart showing the new branches downstream of I1-L803 as determined by the YFull Team: https://app.box.com/s/w9qhdt8b1hxaas37cqwp I have added some notes to the chart to show most distant ancestor timeframe and geographical locations, but will mention an important point here as well: Family Tree DNA did not report any of our 15 Big Y testers as being derived for the novel variant 14888161. However, when the YFull Team analysed the BAMs they identified four L803 men with reads at this position. YFull named the new SNP Y3239. The read details at 14888161 are as follows: Kit 181118 / YF01508: 3 reads = 3T: C>T Kit 150485 / YF01541: 3 reads = 3T: C>T Kit 136903 / YF01597: 2 reads = 2T: C>T Kit 84205 / YF01603: 1 read = 1T: C>T As can be seen on the chart, and despite the scant number of reads, Y3239 (14888161) appears to be an important gateway SNP to further branches downstream. Unfortunately, with the ‘no reads’ at this position, we cannot determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and Frame 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is waiting for a BAM). Has anyone else faced this situation? If so, would FTDNA likely be open to rechecking these kits at 14888161? I don’t have any idea of the the Lab process so this may not be feasible, but I sure would like something definite rather than being left with this ambiguity. There are other L803 members in the Project who did not test Big Y that might also benefit if they could test Y3239 (14888161) – however, what would be my chances of requesting FTDNA to add this SNP to their catalogue when it didn’t even get reported for some of these L803s as a Big Y novel variant? I am a bit bewildered by this situation. The other branch below L803 is L802 – both of these SNPs discovered in Kit 64529’s WTY. Now with Big Y we have another branch parallel to L802 (Y3239) that seems to be taking in many of the L803 families. The maximum GD between any L803 men is 18 at 111 markers – one L802+ and the other Y3239+. I highlighted them with red arrows on the chart. Interestingly, there is only GD 3 between the other L802 and the family of a Y3238 man – also shown with red arrows. Huge variation. Once again, my sincere appreciation to the YFull Team. Kind regards Julie Frame Falk (Admin) Frame / Freame / Fremault DNA Project ------------------------------- To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

BigY coverage could be the explanation. BigY does not just measure 10 million sites in a continuous row. They measure many hundreds, indeed thousands, of Y segments each hundreds of sites long but separated from the next segment by a stretch of unread sites. I checked my coverage and another I have and we both do not cover that site. My coverage starts at 14888279 and the other fellow's coverage starts at 14888220. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Julie Frame Falk Sent: Monday, May 26, 2014 5:00 AM To: I1-Z58andZ63 Project ; Y-DNA Haplogroup I Subject: [yDNAhgI] YFull Interpretation - new branches in I1-L803 Dear Lists Many thanks to the YFull team for their wonderful interpretation service. Some kits have not had processing finalised as yet, but the YFull Experimental Tree suggests it might be timely for me to post an update for the I1-L803 sector. Thus far, nine of our 15 Big Y testers are members of the I1-Z60 project at YFull. Herewith a link to a chart showing the new branches downstream of I1-L803 as determined by the YFull Team: https://app.box.com/s/w9qhdt8b1hxaas37cqwp I have added some notes to the chart to show most distant ancestor timeframe and geographical locations, but will mention an important point here as well: Family Tree DNA did not report any of our 15 Big Y testers as being derived for the novel variant 14888161. However, when the YFull Team analysed the BAMs they identified four L803 men with reads at this position. YFull named the new SNP Y3239. The read details at 14888161 are as follows: Kit 181118 / YF01508: 3 reads = 3T: C>T Kit 150485 / YF01541: 3 reads = 3T: C>T Kit 136903 / YF01597: 2 reads = 2T: C>T Kit 84205 / YF01603: 1 read = 1T: C>T As can be seen on the chart, and despite the scant number of reads, Y3239 (14888161) appears to be an important gateway SNP to further branches downstream. Unfortunately, with the ‘no reads’ at this position, we cannot determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and Frame 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is waiting for a BAM). Has anyone else faced this situation? If so, would FTDNA likely be open to rechecking these kits at 14888161? I don’t have any idea of the the Lab process so this may not be feasible, but I sure would like something definite rather than being left with this ambiguity. There are other L803 members in the Project who did not test Big Y that might also benefit if they could test Y3239 (14888161) – however, what would be my chances of requesting FTDNA to add this SNP to their catalogue when it didn’t even get reported for some of these L803s as a Big Y novel variant? I am a bit bewildered by this situation. The other branch below L803 is L802 – both of these SNPs discovered in Kit 64529’s WTY. Now with Big Y we have another branch parallel to L802 (Y3239) that seems to be taking in many of the L803 families. The maximum GD between any L803 men is 18 at 111 markers – one L802+ and the other Y3239+. I highlighted them with red arrows on the chart. Interestingly, there is only GD 3 between the other L802 and the family of a Y3238 man – also shown with red arrows. Huge variation. Once again, my sincere appreciation to the YFull Team. Kind regards Julie Frame Falk (Admin) Frame / Freame / Fremault DNA Project ------------------------------- To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

I am not sure what you are saying other than 14888161 should be added to the tree? L803 from BigY shows a horde of new snps unique to but common to all or most all the clade. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Julie Frame Falk Sent: Monday, May 26, 2014 5:00 AM To: I1-Z58andZ63 Project ; Y-DNA Haplogroup I Subject: [yDNAhgI] YFull Interpretation - new branches in I1-L803 Dear Lists Many thanks to the YFull team for their wonderful interpretation service. Some kits have not had processing finalised as yet, but the YFull Experimental Tree suggests it might be timely for me to post an update for the I1-L803 sector. Thus far, nine of our 15 Big Y testers are members of the I1-Z60 project at YFull. Herewith a link to a chart showing the new branches downstream of I1-L803 as determined by the YFull Team: https://app.box.com/s/w9qhdt8b1hxaas37cqwp I have added some notes to the chart to show most distant ancestor timeframe and geographical locations, but will mention an important point here as well: Family Tree DNA did not report any of our 15 Big Y testers as being derived for the novel variant 14888161. However, when the YFull Team analysed the BAMs they identified four L803 men with reads at this position. YFull named the new SNP Y3239. The read details at 14888161 are as follows: Kit 181118 / YF01508: 3 reads = 3T: C>T Kit 150485 / YF01541: 3 reads = 3T: C>T Kit 136903 / YF01597: 2 reads = 2T: C>T Kit 84205 / YF01603: 1 read = 1T: C>T As can be seen on the chart, and despite the scant number of reads, Y3239 (14888161) appears to be an important gateway SNP to further branches downstream. Unfortunately, with the ‘no reads’ at this position, we cannot determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and Frame 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is waiting for a BAM). Has anyone else faced this situation? If so, would FTDNA likely be open to rechecking these kits at 14888161? I don’t have any idea of the the Lab process so this may not be feasible, but I sure would like something definite rather than being left with this ambiguity. There are other L803 members in the Project who did not test Big Y that might also benefit if they could test Y3239 (14888161) – however, what would be my chances of requesting FTDNA to add this SNP to their catalogue when it didn’t even get reported for some of these L803s as a Big Y novel variant? I am a bit bewildered by this situation. The other branch below L803 is L802 – both of these SNPs discovered in Kit 64529’s WTY. Now with Big Y we have another branch parallel to L802 (Y3239) that seems to be taking in many of the L803 families. The maximum GD between any L803 men is 18 at 111 markers – one L802+ and the other Y3239+. I highlighted them with red arrows on the chart. Interestingly, there is only GD 3 between the other L802 and the family of a Y3238 man – also shown with red arrows. Huge variation. Once again, my sincere appreciation to the YFull Team. Kind regards Julie Frame Falk (Admin) Frame / Freame / Fremault DNA Project ------------------------------- To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

For starters, I'd inquire of Dr Krahn at his new company www.yseq.net whether he would add 14888161 to his catalog? He likely will. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Julie Frame Falk Sent: Monday, May 26, 2014 5:00 AM To: I1-Z58andZ63 Project ; Y-DNA Haplogroup I Subject: [yDNAhgI] YFull Interpretation - new branches in I1-L803 Dear Lists Many thanks to the YFull team for their wonderful interpretation service. Some kits have not had processing finalised as yet, but the YFull Experimental Tree suggests it might be timely for me to post an update for the I1-L803 sector. Thus far, nine of our 15 Big Y testers are members of the I1-Z60 project at YFull. Herewith a link to a chart showing the new branches downstream of I1-L803 as determined by the YFull Team: https://app.box.com/s/w9qhdt8b1hxaas37cqwp I have added some notes to the chart to show most distant ancestor timeframe and geographical locations, but will mention an important point here as well: Family Tree DNA did not report any of our 15 Big Y testers as being derived for the novel variant 14888161. However, when the YFull Team analysed the BAMs they identified four L803 men with reads at this position. YFull named the new SNP Y3239. The read details at 14888161 are as follows: Kit 181118 / YF01508: 3 reads = 3T: C>T Kit 150485 / YF01541: 3 reads = 3T: C>T Kit 136903 / YF01597: 2 reads = 2T: C>T Kit 84205 / YF01603: 1 read = 1T: C>T As can be seen on the chart, and despite the scant number of reads, Y3239 (14888161) appears to be an important gateway SNP to further branches downstream. Unfortunately, with the ‘no reads’ at this position, we cannot determine if Hamilton 8048 / YF01507, Scruggs 16435 / YF01547, and Frame 110238 / YF01617 are L803* or Y3239* (another Hamilton C kit is waiting for a BAM). Has anyone else faced this situation? If so, would FTDNA likely be open to rechecking these kits at 14888161? I don’t have any idea of the the Lab process so this may not be feasible, but I sure would like something definite rather than being left with this ambiguity. There are other L803 members in the Project who did not test Big Y that might also benefit if they could test Y3239 (14888161) – however, what would be my chances of requesting FTDNA to add this SNP to their catalogue when it didn’t even get reported for some of these L803s as a Big Y novel variant? I am a bit bewildered by this situation. The other branch below L803 is L802 – both of these SNPs discovered in Kit 64529’s WTY. Now with Big Y we have another branch parallel to L802 (Y3239) that seems to be taking in many of the L803 families. The maximum GD between any L803 men is 18 at 111 markers – one L802+ and the other Y3239+. I highlighted them with red arrows on the chart. Interestingly, there is only GD 3 between the other L802 and the family of a Y3238 man – also shown with red arrows. Huge variation. Once again, my sincere appreciation to the YFull Team. Kind regards Julie Frame Falk (Admin) Frame / Freame / Fremault DNA Project ------------------------------- To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Thanks John. My last in that series is an Indel FGC15152 with my private SNPs commencing at FGC15115. On Sun, May 25, 2014 at 4:47 PM, John M Rhodes <johnmrhodes409@gmail.com>wrote: > Hi Wayne, I only found 1 of 17 in YBROWSE > 25095052 FGC7561 > > John M Rhodes > > On 2014-05-25, at 12:54 AM, "Wayne R. Roberts" <i.m223.roberts@gmail.com> > wrote: > > > Here are some from my Full Genomes. They do not appear to be in Ybrowse > > just yet. > > > > 22572691 C T FGC15138+ 22824324 T G FGC15139+ 23253112 T C > > FGC15140+ 23264268 A G FGC15141+ 23366266 G T FGC15142+ 23654782 > C > > T FGC15143+ > > > > > > On Sun, May 25, 2014 at 5:09 AM, John M Rhodes <johnmrhodes409@gmail.com > >wrote: > > > >> Thank you, John. > >> > >> John M Rhodes > >> > >> On 2014-05-24, at 2:40 PM, "John O'Grady" <john_ogrady@outlook.com> > wrote: > >> > >>> It is part of the ISOGG web site: > >>> > >>> http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/ > >>> > >>> ---------------------------------------- > >>>> > >>>> Where is YBROWSE? > >>>> > >>>> John M Rhodes > >>> > >>> > >>> > >>> ------------------------------- > >>> To unsubscribe from the list, please send an email to > >> Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > >> without the quotes in the subject and the body of the message > >> > >> > >> ------------------------------- > >> To unsubscribe from the list, please send an email to > >> Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > >> without the quotes in the subject and the body of the message > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Here are some from my Full Genomes. They do not appear to be in Ybrowse just yet. 22572691 C T FGC15138+ 22824324 T G FGC15139+ 23253112 T C FGC15140+ 23264268 A G FGC15141+ 23366266 G T FGC15142+ 23654782 C T FGC15143+ On Sun, May 25, 2014 at 5:09 AM, John M Rhodes <johnmrhodes409@gmail.com>wrote: > Thank you, John. > > John M Rhodes > > On 2014-05-24, at 2:40 PM, "John O'Grady" <john_ogrady@outlook.com> wrote: > > > It is part of the ISOGG web site: > > > > http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/ > > > > ---------------------------------------- > >> > >> Where is YBROWSE? > >> > >> John M Rhodes > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

For those that have signed up for Yfull, when you log on you can download several csv-files. Among these are: (1) If I go to my ³SNPs² page I can download a csv-file named: ³SNP_for_YF0[ID#]_YYYYMMDD.csv² - If I import this into Excel there are three columns: (a) SNP Name (b) Call (positive/negative/no call) (c) Comment (³1 read!²) (2) If I go to my ³Private SNPs² page I can download a csv-file named: ³PrivateSNP_for_YF0[ID#]_YYYYMMDD.csv² - If I import this into Excel there are five columns: (a) SNP Name (b) Position (c) Reference (d) Derived (e) Quality There are almost 53,000 SNPs in my SNP file; If I go to my ³Check SNPs² page and input a SNP name, I can get a full and complete analysis of that SNP, including ³ChrY position.² Currently, the SNP result file (#1 above) does NOT include the position of the SNP making comparisons between people in a particular project complicated. If we could get the results for the SNP file in the same format as the Private SNP file it would be ideal. May I suggest that anyone who has signed up for Yfull request that the SNP file be formatted like the Private SNPs file. To contact them you have to look at the very bottom of the page, in VERY small letters,for ³Feedback² to send them a message. The format of these two files I recommend that we all request that they supply the SNP-file

Hi Wayne, I only found 1 of 17 in YBROWSE 25095052 FGC7561 John M Rhodes On 2014-05-25, at 12:54 AM, "Wayne R. Roberts" <i.m223.roberts@gmail.com> wrote: > Here are some from my Full Genomes. They do not appear to be in Ybrowse > just yet. > > 22572691 C T FGC15138+ 22824324 T G FGC15139+ 23253112 T C > FGC15140+ 23264268 A G FGC15141+ 23366266 G T FGC15142+ 23654782 C > T FGC15143+ > > > On Sun, May 25, 2014 at 5:09 AM, John M Rhodes <johnmrhodes409@gmail.com>wrote: > >> Thank you, John. >> >> John M Rhodes >> >> On 2014-05-24, at 2:40 PM, "John O'Grady" <john_ogrady@outlook.com> wrote: >> >>> It is part of the ISOGG web site: >>> >>> http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/ >>> >>> ---------------------------------------- >>>> >>>> Where is YBROWSE? >>>> >>>> John M Rhodes >>> >>> >>> >>> ------------------------------- >>> To unsubscribe from the list, please send an email to >> Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' >> without the quotes in the subject and the body of the message >> >> >> ------------------------------- >> To unsubscribe from the list, please send an email to >> Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' >> without the quotes in the subject and the body of the message > > ------------------------------- > To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Thanks Kenneth, iam going to check it out. greatings Stefan 2014-05-24 18:20 GMT+02:00 Kenneth Nordtvedt <knordtvedt@bresnan.net>: > I have put a new sector tree “ BigYtree-L813” on my website with all shown > snps being weeded. > > Main significant structure is the massive split done only with severeal > brand new snps. > I see no geographical significance yet for this massive split. > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message

I have put on my website preliminary tree of BigY snps for Z63 sector of I1. I don’t yet have the unique weeded snps for each terminal line; just the weeded upstream snps shared by two or more Z63 people are presently shown. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net

Thank you, John. John M Rhodes On 2014-05-24, at 2:40 PM, "John O'Grady" <john_ogrady@outlook.com> wrote: > It is part of the ISOGG web site: > > http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/ > > ---------------------------------------- >> >> Where is YBROWSE? >> >> John M Rhodes > > > > ------------------------------- > To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Where is YBROWSE? John M Rhodes On 2014-05-24, at 1:42 PM, Obed W Odom <owodom@utexas.edu> wrote: > Ken, to search YBrowse by location, for example for location 22208780, you > need to enter "Chry:22208780..22208780" (without the quotation marks) in > the search box. When I did this, it showed that FGC9495 is at this > location. Then, by clicking on FGC9495 a new window opens showing that > FGC9495 is a C to A mutation found by Full Genomes in 2014. > > > On Sat, May 24, 2014 at 11:49 AM, Kenneth Nordtvedt > <knordtvedt@bresnan.net>wrote: > >> They can be seen as the first major division of "BigYtree-L813" >> >> 22208780 >> 21657006 >> 21426337 >> 18949040 >> 8035203 >> 8208733 >> 8839135 >> 14522697 >> 17082329 >> 18593683 >> >> >> >> Kenneth Nordtvedt > > ------------------------------- > To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Not many groups yet as it was just introduced a few months ago. But it is included, for example, in the UCSC Genome Browser: http://genome.ucsc.edu On Sat, May 24, 2014 at 1:52 PM, Kenneth Nordtvedt <knordtvedt@bresnan.net>wrote: > So who is using b38? > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: G. Magoon > Sent: Saturday, May 24, 2014 11:48 AM > To: y-dna-haplogroup-i > Subject: Re: [yDNAhgI] FGC and Y series snps > > The location numbers that you are using (based on b37) have already changed > with the recent introduction of b38 and there will almost certainly be > further changes as the reference sequence is further refined. > > > On Sat, May 24, 2014 at 1:35 PM, Kenneth Nordtvedt > <knordtvedt@bresnan.net>wrote: > > > I certainly DON'T want snp names as such; I believe location numbers are > > best names for sure which will never change. Keeping a limited number of > > historically significant early snp names is OK, but the naming process > > should stop in my opinion. > > > > > > > > Kenneth Nordtvedt > > > > Haplogroup I Clade Modalities and Trees at: > > http://knordtvedt.home.bresnan.net > > > > -----Original Message----- > > From: John O'Grady > > Sent: Saturday, May 24, 2014 11:10 AM > > To: y-dna-haplogroup-i@rootsweb.com > > Subject: Re: [yDNAhgI] FGC and Y series snps > > > > If you want SNP names, people need to send their BAM files to YFull > and/or > > FGC for analysis. It costs $50, but it would make your job a lot easier. > > > > John O'Grady > > > > ---------------------------------------- > > > > > > Can't yet put in location and get snp. But scrolling will allow > location > > > to > > > find name easy enough. 10 new snps divide L813 sector of I1 tree. Not > > > one > > > of them is listed in FGC series or any other series for that matter. > > > Strange. > > > > > > > > > > > > Kenneth Nordtvedt > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > > without > > the quotes in the subject and the body of the message > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

The location numbers that you are using (based on b37) have already changed with the recent introduction of b38 and there will almost certainly be further changes as the reference sequence is further refined. On Sat, May 24, 2014 at 1:35 PM, Kenneth Nordtvedt <knordtvedt@bresnan.net>wrote: > I certainly DON'T want snp names as such; I believe location numbers are > best names for sure which will never change. Keeping a limited number of > historically significant early snp names is OK, but the naming process > should stop in my opinion. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: John O'Grady > Sent: Saturday, May 24, 2014 11:10 AM > To: y-dna-haplogroup-i@rootsweb.com > Subject: Re: [yDNAhgI] FGC and Y series snps > > If you want SNP names, people need to send their BAM files to YFull and/or > FGC for analysis. It costs $50, but it would make your job a lot easier. > > John O'Grady > > ---------------------------------------- > > > > Can't yet put in location and get snp. But scrolling will allow location > > to > > find name easy enough. 10 new snps divide L813 sector of I1 tree. Not one > > of them is listed in FGC series or any other series for that matter. > > Strange. > > > > > > > > Kenneth Nordtvedt > > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > Y-DNA-HAPLOGROUP-I-request@rootsweb.com with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

That would be Archerd, the original poster. On Fri, May 23, 2014 at 2:20 PM, Kenneth Nordtvedt <knordtvedt@bresnan.net>wrote: > Who has the evidence S6346 is split upstream from L22. I kinow it is > downstream of CTS10028? > >