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

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

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

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

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

Hi Richard Thanks so much for your explanation of the testing and filtering process. Very much appreciated! <<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. >> I am so pleased we opted to have YFull analyse our 15 x L803 BAM files Richard. I believe we would have missed out on so much if we hadn’t...including all of the additional STRs! Interestingly, I found that FTDNA report some novel variants with low reads, well under the 55 – 80 reads that you mention. FTDNA only reported two of our L803 kits: 136903 and 76423 as being derived for the novel variant 7519928. YFull named this new SNP Y3456. At the YFull website I am able to determine that: Kit 136903 / YF01597 had 32 reads = 32G A > G Kit 76423 / YF01495 only had 10 reads (10 reads = 10G A > G) yet was still reported derived by FTDNA. Going by their Tree, YFull finds an additional two of our L803 Big Y testers positive for this new SNP but so far I can only check the number of reads for one. This man, Kit 227254 / YF01598, actually had 6 reads at 7519928 (6G A > G ) yet he was filtered out at FTDNA. So maybe FTDNA filter out anything under 10 reads? Just on the numbers from my L802 brother’s BAM file, YFull shows he was positive for 1360 SNPs, had No Calls for 14206 and 244 were Ambiguous. He also has a Best Quality private SNP at 21070711 (YFS099079) - he doesn’t mind me disclosing that info. For now, all I can say re our other L803 Big Y testers is that quite a number of them have new private SNPs and Indels. They may be very useful in the years ahead. Thanks again for your comments, Richard. I will keep pursuing this! Kindest regards Julie Frame Falk From: DNAresults Sent: Tuesday, May 27, 2014 5:37 AM To: Julie Frame Falk ; y-dna-haplogroup-i@rootsweb.com Subject: Re: [yDNAhgI] YFull Interpretation - new branches in I1-L803 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