> My test found 67 > new SNPs and 1 new indel in the "highly reliable" category, How do testing companies report new SNPs? Do they give each one a letter and number designation like other well known SNPs and how do they determine if a SNP is a "private" or "family" SNP as opposed to one which might be used to designate a new haplogroup? I'm also curious as to whether all the SNP results will be reported online for the Big Y so that everyone can inspect them? Matthew Simonds > Date: Sat, 4 Jan 2014 18:24:46 -0600 > From: [email protected] > To: [email protected] > Subject: Re: [yDNAhgI] PF3514 > > I think the Big Y will be done with next-generation sequencing so it should > be somewhat comparable to the Full Genomes test. We don't yet know, > however, how good the coverage will be. My Full Genomes coverage averaged > about 50x; i.e,, an average of about 50 reads for each location looked at, > but this varied from about 5 to 100 reads per location. My test found 67 > new SNPs and 1 new indel in the "highly reliable" category, and these > seemed to be spread out fairly uniformly over a 14 to 15 million base pair > region, including locations from 4 to 9.5 million, 13.6 to 23.2 million, > and a short stretch around 28.5 million. My raw data BAM file has a size of > 12 gb, but the analysis team at Full Genomes talked me through the > procedure for downloading it using the wget utility, which turned out to be > fairly easy. I can now view my raw data against the human reference > sequence using the IGV > viewer. > > > On Sat, Jan 4, 2014 at 5:40 PM, Matthew Simonds <[email protected]>wrote: > > > > > >so I have yet to see a next-generation-sequencing sample with G at this > > site. > > > > > > Will the Big Y all be done with next-generation-sequencing? I heard that > > it will test for 25,000 known SNPs and sequence 10 million base pairs. Will > > the testing for the 25,000 known SNPs also be done with > > next-generation-sequencing or with a chip? > > > > Matthew Simonds > > > > > Date: Sat, 4 Jan 2014 11:52:37 -0600 > > > From: [email protected] > > > To: [email protected] > > > Subject: Re: [yDNAhgI] PF3514 > > > > > > I see that I had the positions of the mismatches between the HUGO > > > reference X and Y sequences slightly off. The mismatch points are 22 > > bases > > > upstream and 32 bases downstream of the PF3514 site. Also, I looked at > > > several I2a samples (HG00360, HG01344, and HG01197) from the 1000 Genomes > > > project and they all show C at the site of PF3514, so I have yet to see a > > > next-generation-sequencing sample with G at this site. > > > > > > > > > On Sat, Jan 4, 2014 at 3:36 AM, G. Magoon <[email protected]> wrote: > > > > > > > Hi Wayne, > > > > You should be able to find results for PF3514 in the genotyping > > ("gtype") > > > > report. > > > > > > > > Nice analysis, Obed! > > > > Greg > > > > On Jan 4, 2014 3:50 AM, "Wayne R. Roberts" <[email protected]> > > > > wrote: > > > > > > > > > Obed, my samples went to UCLA and unfortunately UCLA results were not > > > > > satisfactory. I have sent new samples off to Full Genomes so will > > have to > > > > > wait longer for results. > > > > > > > > > > Do you know what result Adam Waalkes received for PF3514? Ken, Aaron > > and > > > > I > > > > > have all his results data but I'm not so sure how to read the raw > > data > > > > > files. > > > > > > > > > > > > > > > On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> > > wrote: > > > > > > > > > > > Thanks, Wayne. Are you still waiting for your Full Genomes > > results? If > > > > > so, > > > > > > please let us know your result at the site of PF3514 when you > > receive > > > > > them. > > > > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts > > > > > > <[email protected]>wrote: > > > > > > > > > > > > > Obed, my question to Thomas was: > > > > > > > > > > > > > > One of our I-M223 Project members just received his Geno 2.0 > > results. > > > > > He > > > > > > is > > > > > > > from the Project's Continental 2a group CTS6433+. When his raw > > data > > > > is > > > > > > > compared with that of other members he shows PF3514 with A A. All > > > > > others > > > > > > > show A G. Ybrowse has PF3514 mutation as A to G. How should I > > > > interpret > > > > > > his > > > > > > > result? Is he derived and ancestral is actually G or is he > > ancestral > > > > > > (back > > > > > > > mutation) and everyone else is derived? Thanks for any advise, > > Wayne. > > > > > > > > > > > > > > He did not indicate it should be A to C and Ybrowse has A to G. > > > > > > > > > > > > > > > > > > > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> > > > > wrote: > > > > > > > > > > > > > > > Wayne, > > > > > > > > > > > > > > > > Did Thomas explicitly say that the derived value for PF3514 is > > G, > > > > or > > > > > > > could > > > > > > > > it be C? My Full Genomes result clearly shows that I have C at > > this > > > > > > > > location. I looked at the X and Y sequences in this region and > > they > > > > > are > > > > > > > > indeed very similar, but they do differ at points 17 bases > > upstream > > > > > and > > > > > > > 37 > > > > > > > > bases downstream of the PF3514 site, which must be enough for > > Full > > > > > > > Genomes > > > > > > > > to separate the Y and X sequences. Full Genomes shows my X > > sequence > > > > > to > > > > > > be > > > > > > > > identical to the HUGO reference, with A at the > > PF3514-homologous > > > > > site. > > > > > > So > > > > > > > > Geno 2.0 was clearly in error when they reported me as AG > > instead > > > > of > > > > > > AC. > > > > > > > > > > > > > > > > Although I cannot see their raw data, Full Genomes also > > reports > > > > > > several > > > > > > > > other I1 people to have C at this position. These include > > another > > > > > > > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be > > > > > interesting > > > > > > to > > > > > > > > hear what your Full Genomes test showed at the PF3514 site. In > > > > > > particular > > > > > > > > I'm wondering if Full Genomes has shown anyone to have G at the > > > > > PF3514 > > > > > > > > site. I suppose it's possible that those of us who have C have > > had > > > > a > > > > > > > second > > > > > > > > mutation at this site, from G to C. > > > > > > > > > > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > > > > > > > <[email protected]>wrote: > > > > > > > > > > > > > > > > > This is what Thomas had to say about PF3514: > > > > > > > > > > > > > > > > > > Everyone in IJ is supposed to be derived. Actually all others > > > > have > > > > > an > > > > > > > A. > > > > > > > > It > > > > > > > > > seems like the region around PF3514 is very similar to > > > > > > > > > ChrX:91846733..91846902. > > > > > > > > > > > > > > > > > > I've made a comparison here: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > > > > > > > hope this link works for you). > > > > > > > > > > > > > > > > > > The X chromosome has also a "A" at this position and the > > probe on > > > > > the > > > > > > > > Geno2 > > > > > > > > > chip picks them up both. What likely happened is that his > > > > ancestors > > > > > > > were > > > > > > > > > derived for PF3514, but some X-Y recombination event has > > wiped > > > > that > > > > > > > > > mutation out at a later time so that it shows the ancestral > > "A" > > > > > again > > > > > > > at > > > > > > > > > this location. > > > > > > > > > > > > > > > > > > ------------------------------- > > > > > > > > > To unsubscribe from the list, please send an email to > > > > > > > > > [email protected] 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 > > > > > > > > [email protected] 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 > > > > > > > [email protected] 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 > > > > > > [email protected] 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 > > > > > [email protected] 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 > > > > [email protected] 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 > > [email protected] 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 > > [email protected] 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Diana, Two more e-mails have bounced since I received your e-mail this afternoon. Lindsey

For a dna sample to truly be I* it would need to be: 1. Derived for M170 or one of the many other known phyloequivalent snps. 2. Ancestral for M438 and all the 22 or so known phyloequivalent snps. 3. Ancestral for M253 and all the 100 or so known phyloequivalent snps. See "Tree and Map for haplogroup I". There is no dna sample that has been through all that wringer as far as I know. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Matthew Simonds Sent: Sunday, January 05, 2014 2:14 PM To: [email protected] Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans All of these samples in this latest study were I* or I2. What is the oldest sample of I1 yet found? > From: [email protected] > To: [email protected]; [email protected] > Date: Sun, 5 Jan 2014 13:31:02 -0700 > Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans > > Yes, it is a very interesting paper, especially to haplogroup I folks. > Unfortunately they did not go as far as they could have gone because they > limited themselves to ISOGG tree; this situation can maybe be remedied.. > I hope this paper encourages the study of more ancient dna samples from > Europe and from as many different time periods as possible. > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > > From: Didier VERNADE > Sent: Sunday, January 05, 2014 1:23 PM > To: Kenneth Nordtvedt ; [email protected] > Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans > > > OK, tanks for the update ; I hope the link will still be of some use for > other late comers like me ! > > > > > > > > > You apparently have not been tuned in. It has been discusssed rather > > extensively on this list. If you look at "Tree and Map for haplogroup > I" > > and "Tree for L161" you can see some of the very interesting snp > placements > > and new tree branch resulting from testing of many recent snp > discoveries > > from Geno2 on some of these 8000 b.p. dna samples. I think there is > more to > > come if Mortala2 and Mortala9 turn out to be readble for an additional > bunch > > of ysnps presented to them. > > > > > > > > Kenneth Nordtvedt > > > > Haplogroup I Clade Modalities and Trees at: > > http://knordtvedt.home.bresnan.net > > > ------------------------------------------------------------------------------------------------------------------------------ > > It seems that the recent paper, "Ancient human genomes suggest three > > ancestral populations for present-day Europeans" wasn't discussed on > this > > list while the early european seem to be of I haplogroup. Here is a > link : > > > > http://biorxiv.org/content/early/2013/12/23/001552 > > > > > > > > Didier Vernade > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] 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 > [email protected] 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Motala2 and Motala9 are just read to be IxM253 or IxP40. We can really say no more about them from the unread snps. Motala2 reads CTS1293- which by itself does not say much. The * usage is very misleading. Motala12 is very likely identical to Loschbour and maybe even M3. Loschbour is quite specifically located quite a ways downstream. If you are talking about age of dna sample, I don't know what the oldest such sample measured is. I don't think it would be very old. Present day I1 seems to have a MRCA about 4500 years ago, although some people have suggested a slightly older date. There are incredible opportunities for old dna samples splitting the hundred or so known snps phyloequivalent to M253 but whose ages of occurrence span the time period --- 4500 b.p. back to 22,000 b.p. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Matthew Simonds Sent: Sunday, January 05, 2014 2:14 PM To: [email protected] Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans All of these samples in this latest study were I* or I2. What is the oldest sample of I1 yet found? > From: [email protected] > To: [email protected]; [email protected] > Date: Sun, 5 Jan 2014 13:31:02 -0700 > Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans > > Yes, it is a very interesting paper, especially to haplogroup I folks. > Unfortunately they did not go as far as they could have gone because they > limited themselves to ISOGG tree; this situation can maybe be remedied.. > I hope this paper encourages the study of more ancient dna samples from > Europe and from as many different time periods as possible. > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > > From: Didier VERNADE > Sent: Sunday, January 05, 2014 1:23 PM > To: Kenneth Nordtvedt ; [email protected] > Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans > > > OK, tanks for the update ; I hope the link will still be of some use for > other late comers like me ! > > > > > > > > > You apparently have not been tuned in. It has been discusssed rather > > extensively on this list. If you look at "Tree and Map for haplogroup > I" > > and "Tree for L161" you can see some of the very interesting snp > placements > > and new tree branch resulting from testing of many recent snp > discoveries > > from Geno2 on some of these 8000 b.p. dna samples. I think there is > more to > > come if Mortala2 and Mortala9 turn out to be readble for an additional > bunch > > of ysnps presented to them. > > > > > > > > Kenneth Nordtvedt > > > > Haplogroup I Clade Modalities and Trees at: > > http://knordtvedt.home.bresnan.net > > > ------------------------------------------------------------------------------------------------------------------------------ > > It seems that the recent paper, "Ancient human genomes suggest three > > ancestral populations for present-day Europeans" wasn't discussed on > this > > list while the early european seem to be of I haplogroup. Here is a > link : > > > > http://biorxiv.org/content/early/2013/12/23/001552 > > > > > > > > Didier Vernade > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] 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 > [email protected] 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Geno 2.0 raw data is not available anywhere at FTDNA, you have to download it from the geno 2.0 website. Login with your Genographic ID code or your username and password if you created one:: https://genographic.nationalgeographic.com/results/login/userlogin Then go to Profile in the blue bar near the top of the page, then on the new page, click on expert options which will be a tab in a gray bar a little bit farther down the page. Then you should see a DOWNLOAD.CSV button, click on it. The Geno 2.0 website is confusing but you should be able to find it eventualy Bernie

Hello Carol, Thank you for the added information, I've updated his entry: http://dgmweb.net/DNA/matrices/HgI1/HgI1_matrix_M253.html#L69.1 I'm afraid I've never had a male relative take a Geno 2.0 test - two WTY's, but no Geno2's - so I don't know how to read the raw data. In fact, I took the Geno2 test, myself, just so I would be able to answer my project members' questions about it and learn how to read the data files. But I can't even *find* the raw data files at my member page. So, I have to ask the same question: how do we find/download/read the raw data files from our Geno2 tests? Diana > From: Carol Gilbert > Sent: Sunday, January 05, 2014 5:32 AM > To: [email protected] > Subject: Re: [yDNAhgI] L69 / L1274 / L1275 > > Hi Gale, > 267833 is my husband ( no known ancestral surname), adoptive name Gilbert, > and I have - on advice- checked his raw data which indicates he is M227 > negative and he recently tested L1275 which was also negative. Tell me where > to look for the rest, if that is possible, and I'll tell you the answer. > > Carol Gilbert

Yes, it is a very interesting paper, especially to haplogroup I folks. Unfortunately they did not go as far as they could have gone because they limited themselves to ISOGG tree; this situation can maybe be remedied.. I hope this paper encourages the study of more ancient dna samples from Europe and from as many different time periods as possible. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net From: Didier VERNADE Sent: Sunday, January 05, 2014 1:23 PM To: Kenneth Nordtvedt ; [email protected] Subject: Re: [yDNAhgI] 3 ancestral populations for present-day Europeans OK, tanks for the update ; I hope the link will still be of some use for other late comers like me ! > > You apparently have not been tuned in. It has been discusssed rather > extensively on this list. If you look at "Tree and Map for haplogroup I" > and "Tree for L161" you can see some of the very interesting snp placements > and new tree branch resulting from testing of many recent snp discoveries > from Geno2 on some of these 8000 b.p. dna samples. I think there is more to > come if Mortala2 and Mortala9 turn out to be readble for an additional bunch > of ysnps presented to them. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > ------------------------------------------------------------------------------------------------------------------------------ > It seems that the recent paper, "Ancient human genomes suggest three > ancestral populations for present-day Europeans" wasn't discussed on this > list while the early european seem to be of I haplogroup. Here is a link : > > http://biorxiv.org/content/early/2013/12/23/001552 > > > > Didier Vernade > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message > >

You apparently have not been tuned in. It has been discusssed rather extensively on this list. If you look at "Tree and Map for haplogroup I" and "Tree for L161" you can see some of the very interesting snp placements and new tree branch resulting from testing of many recent snp discoveries from Geno2 on some of these 8000 b.p. dna samples. I think there is more to come if Mortala2 and Mortala9 turn out to be readble for an additional bunch of ysnps presented to them. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Didier VERNADE Sent: Sunday, January 05, 2014 1:04 PM To: y-dna-haplogroup-i Subject: [yDNAhgI] 3 ancestral populations for present-day Europeans It seems that the recent paper, "Ancient human genomes suggest three ancestral populations for present-day Europeans" wasn't discussed on this list while the early european seem to be of I haplogroup. Here is a link : http://biorxiv.org/content/early/2013/12/23/001552 Didier Vernade ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Ken, As you know I am AS3, Z382. My Geno2 results for CTS2729 and CTS8649 are GG and GG. I don't know if these are ancestral or derived. George Doty (43947)

Hi Gale, 267833 is my husband ( no known ancestral surname), adoptive name Gilbert, and I have - on advice- checked his raw data which indicates he is M227 negative and he recently tested L1275 which was also negative. Tell me where to look for the rest, if that is possible, and I'll tell you the answer. Carol Gilbert [email protected] On 5 Jan 2014, at 01:04, Diana Gale Matthiesen wrote: > I've been trying to glean from the SNP Results tables at FTDNA and the archive > of this list just who among the CTS6364+ individuals has tested positive for any > one of these SNPs: L69, M227, L1274, and L1275. This is what I have found, so > far. > > L69 > N20789 ROBESON..... L69+ L1274- L1275- M227- > _80366 RHODES...... L69+ L1274- L1275- M227- > 119706 DAY......... L69+ ______ ______ M227- > 181124 McISAAC..... L69+ ______ L1275- _____ > 132649 PIOTROWIZC.. L69+ ______ ______ _____ > N95371 HASLE....... L69+ L1274- L1275- _____ > _20551 HIGHT....... L69+ ______ L1275- M227- > 275994 MYKLEBUST... L69+ ______ ______ _____ > 267833 ?........... L69+ ______ ______ _____ > 105394 SKARBEK..... L69+ L1274- L1274- _____ > > If you are L69+ and haven't tested M227, you might want to consider doing so. > It's actually somewhat amazing to find anyone escape getting an M227 test as > part of FTDNA's "Deep SNP" test. > > L69 > M227 > Only two of the 15 M227+'s have tested L69: > _66586 AZZI........ L69+ ______ ______ > 213344 PROKOPIUK... L69+ ______ ______ > > The PROKOPIUK is taking the BigY, so we should soon have his results for > L1274/L1275. > > L69? > L1275 > _21268 ALLRED...... ____ L1274- L1275+ > 122425 BRITTON..... ____ ______ L1275+ > > How was L1275 placed downstream of L69 if neither of these individuals tested > it? > > L69 > L1274 > Neither of the CHILDERS appears to have tested L1275: > 19389 CHILDERS..... L69+ ______ ______ > 78040 CHILDRESS.... ____ L1274+ ______ > > If you have taken any of these tests, and I have omitted your results, please > share. > > Diana > > P.S. I am not suggesting anyone who is taking the BigY do any a la carte SNP > testing at this point. Only if you have no intention of taking one of the > "deep" SNP tests, now or in the near future, should you consider a la carte SNP > testing. > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

George, You have the ancestral values for both. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: george doty Sent: Sunday, January 05, 2014 9:06 AM To: [email protected] Subject: [yDNAhgI] I1 AS3 Z382+ Clade has 2 Neglected SNPs Ken, As you know I am AS3, Z382. My Geno2 results for CTS2729 and CTS8649 are GG and GG. I don't know if these are ancestral or derived. George Doty (43947) ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Diana, I replied to your e-mail twice, using the reply button and both replies have bounced. Lindsey

Companies create a prefix to identify the SNPs they report. For instance, Full Genomes uses the prefix FGC. A SNP is considered private if only one person is derived for it. Geno 2.0 results are currently listed on FTDNA project pages. We will have to wait and see if FTDNA does the same with Big Y results. John O'Grady > > How do testing companies report new SNPs? Do they give each one a letter and number designation like other well known SNPs and how do they determine if a SNP is a "private" or "family" SNP as opposed to one which might be used to designate a new haplogroup? I'm also curious as to whether all the SNP results will be reported online for the Big Y so that everyone can inspect them? > > Matthew Simonds

Am I correct that it was CHILDERS #19389 who took the WTY? He's not showing any SNPs at FTDNA, so can someone tell me, please, whether or not he was positive for all of these? M253 DF29 CTS6364 L69 L1275 L1274 Diana

>so I have yet to see a next-generation-sequencing sample with G at this site. Will the Big Y all be done with next-generation-sequencing? I heard that it will test for 25,000 known SNPs and sequence 10 million base pairs. Will the testing for the 25,000 known SNPs also be done with next-generation-sequencing or with a chip? Matthew Simonds > Date: Sat, 4 Jan 2014 11:52:37 -0600 > From: [email protected] > To: [email protected] > Subject: Re: [yDNAhgI] PF3514 > > I see that I had the positions of the mismatches between the HUGO > reference X and Y sequences slightly off. The mismatch points are 22 bases > upstream and 32 bases downstream of the PF3514 site. Also, I looked at > several I2a samples (HG00360, HG01344, and HG01197) from the 1000 Genomes > project and they all show C at the site of PF3514, so I have yet to see a > next-generation-sequencing sample with G at this site. > > > On Sat, Jan 4, 2014 at 3:36 AM, G. Magoon <[email protected]> wrote: > > > Hi Wayne, > > You should be able to find results for PF3514 in the genotyping ("gtype") > > report. > > > > Nice analysis, Obed! > > Greg > > On Jan 4, 2014 3:50 AM, "Wayne R. Roberts" <[email protected]> > > wrote: > > > > > Obed, my samples went to UCLA and unfortunately UCLA results were not > > > satisfactory. I have sent new samples off to Full Genomes so will have to > > > wait longer for results. > > > > > > Do you know what result Adam Waalkes received for PF3514? Ken, Aaron and > > I > > > have all his results data but I'm not so sure how to read the raw data > > > files. > > > > > > > > > On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> wrote: > > > > > > > Thanks, Wayne. Are you still waiting for your Full Genomes results? If > > > so, > > > > please let us know your result at the site of PF3514 when you receive > > > them. > > > > > > > > > > > > On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts > > > > <[email protected]>wrote: > > > > > > > > > Obed, my question to Thomas was: > > > > > > > > > > One of our I-M223 Project members just received his Geno 2.0 results. > > > He > > > > is > > > > > from the Project's Continental 2a group CTS6433+. When his raw data > > is > > > > > compared with that of other members he shows PF3514 with A A. All > > > others > > > > > show A G. Ybrowse has PF3514 mutation as A to G. How should I > > interpret > > > > his > > > > > result? Is he derived and ancestral is actually G or is he ancestral > > > > (back > > > > > mutation) and everyone else is derived? Thanks for any advise, Wayne. > > > > > > > > > > He did not indicate it should be A to C and Ybrowse has A to G. > > > > > > > > > > > > > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> > > wrote: > > > > > > > > > > > Wayne, > > > > > > > > > > > > Did Thomas explicitly say that the derived value for PF3514 is G, > > or > > > > > could > > > > > > it be C? My Full Genomes result clearly shows that I have C at this > > > > > > location. I looked at the X and Y sequences in this region and they > > > are > > > > > > indeed very similar, but they do differ at points 17 bases upstream > > > and > > > > > 37 > > > > > > bases downstream of the PF3514 site, which must be enough for Full > > > > > Genomes > > > > > > to separate the Y and X sequences. Full Genomes shows my X sequence > > > to > > > > be > > > > > > identical to the HUGO reference, with A at the PF3514-homologous > > > site. > > > > So > > > > > > Geno 2.0 was clearly in error when they reported me as AG instead > > of > > > > AC. > > > > > > > > > > > > Although I cannot see their raw data, Full Genomes also reports > > > > several > > > > > > other I1 people to have C at this position. These include another > > > > > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be > > > interesting > > > > to > > > > > > hear what your Full Genomes test showed at the PF3514 site. In > > > > particular > > > > > > I'm wondering if Full Genomes has shown anyone to have G at the > > > PF3514 > > > > > > site. I suppose it's possible that those of us who have C have had > > a > > > > > second > > > > > > mutation at this site, from G to C. > > > > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > > > > > <[email protected]>wrote: > > > > > > > > > > > > > This is what Thomas had to say about PF3514: > > > > > > > > > > > > > > Everyone in IJ is supposed to be derived. Actually all others > > have > > > an > > > > > A. > > > > > > It > > > > > > > seems like the region around PF3514 is very similar to > > > > > > > ChrX:91846733..91846902. > > > > > > > > > > > > > > I've made a comparison here: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > > > > > hope this link works for you). > > > > > > > > > > > > > > The X chromosome has also a "A" at this position and the probe on > > > the > > > > > > Geno2 > > > > > > > chip picks them up both. What likely happened is that his > > ancestors > > > > > were > > > > > > > derived for PF3514, but some X-Y recombination event has wiped > > that > > > > > > > mutation out at a later time so that it shows the ancestral "A" > > > again > > > > > at > > > > > > > this location. > > > > > > > > > > > > > > ------------------------------- > > > > > > > To unsubscribe from the list, please send an email to > > > > > > > [email protected] 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 > > > > > > [email protected] 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 > > > > > [email protected] 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 > > > > [email protected] 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 > > > [email protected] 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 > > [email protected] 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Do the probabilities at Family Tree DNA for TMRCA between two men based on STR markers also hold true even if the two men do not share the same surname? When describing what matching at the 67 marker level means, Family Tree DNA prefaces their statement by saying, "A XX/67 match between two men who share a common surname (or variant) means...". So I'm not sure how accurate STR matching probabilities are for two men with different surnames but who share the same Haplogroup, i.e. I-P109. Does the fact that we don't share a common surname change the probabilities for TMRCA in any way based on STR matching? At the 67 marker level, I only have matching with two men who do not share my surname. My surname is Simonds, and based on 67 markers, Family Tree DNA says that I have a 98.7% probability of sharing a common ancestor with someone named Lambert within the last 24 generations which I would calculate at about 720 years or 30 years per generation. It says that I have a 99.72% probability of sharing a common ancestor with someone with the surname Diver within the last 24 generations. It's interesting to me that these two families, the Diver and the Lambert families, lived within less than 10 miles of each other in the early 17th century. The ancestor of Diver (kit # 42300) was baptized at Isleham, Cambridgeshire in 1618 while the ancestor of Lambert (kit 206903) was supposedly married at Cavenham, Suffolk in 1624. Isleham, Cambridgeshire and Cavenham, Suffolk are (according to Google Maps only about 9.9 miles from each other. My own ancestor William Simonds was born in England in 1611, although I don't know for sure where in England he came from. But I had already thought even before I did any DNA testing that he might have come from Suffolk since there are many Simonds/Symonds families who were living there since at least the beginning of the 15th century. Can I assume based on my STR matching with the Diver and Lambert families that my own Simonds family did indeed come from this same area of East Anglia and that the Diver, Lambert and Simonds families had a common paternal ancestor there within at least the last 720 years or sometime in the 1200s? Matthew Simonds P.S. For purposes of comparison with someone from my own surname, I have a match with someone that I know to be my 9th cousin with ten generation separating us. Family Tree DNA says that we have an 88.29% probability of sharing a common ancestor within the last 12 generations.

I've been trying to glean from the SNP Results tables at FTDNA and the archive of this list just who among the CTS6364+ individuals has tested positive for any one of these SNPs: L69, M227, L1274, and L1275. This is what I have found, so far. L69 N20789 ROBESON..... L69+ L1274- L1275- M227- _80366 RHODES...... L69+ L1274- L1275- M227- 119706 DAY......... L69+ ______ ______ M227- 181124 McISAAC..... L69+ ______ L1275- _____ 132649 PIOTROWIZC.. L69+ ______ ______ _____ N95371 HASLE....... L69+ L1274- L1275- _____ _20551 HIGHT....... L69+ ______ L1275- M227- 275994 MYKLEBUST... L69+ ______ ______ _____ 267833 ?........... L69+ ______ ______ _____ 105394 SKARBEK..... L69+ L1274- L1274- _____ If you are L69+ and haven't tested M227, you might want to consider doing so. It's actually somewhat amazing to find anyone escape getting an M227 test as part of FTDNA's "Deep SNP" test. L69 > M227 Only two of the 15 M227+'s have tested L69: _66586 AZZI........ L69+ ______ ______ 213344 PROKOPIUK... L69+ ______ ______ The PROKOPIUK is taking the BigY, so we should soon have his results for L1274/L1275. L69? > L1275 _21268 ALLRED...... ____ L1274- L1275+ 122425 BRITTON..... ____ ______ L1275+ How was L1275 placed downstream of L69 if neither of these individuals tested it? L69 > L1274 Neither of the CHILDERS appears to have tested L1275: 19389 CHILDERS..... L69+ ______ ______ 78040 CHILDRESS.... ____ L1274+ ______ If you have taken any of these tests, and I have omitted your results, please share. Diana P.S. I am not suggesting anyone who is taking the BigY do any a la carte SNP testing at this point. Only if you have no intention of taking one of the "deep" SNP tests, now or in the near future, should you consider a la carte SNP testing.

Obed, my samples went to UCLA and unfortunately UCLA results were not satisfactory. I have sent new samples off to Full Genomes so will have to wait longer for results. Do you know what result Adam Waalkes received for PF3514? Ken, Aaron and I have all his results data but I'm not so sure how to read the raw data files. On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> wrote: > Thanks, Wayne. Are you still waiting for your Full Genomes results? If so, > please let us know your result at the site of PF3514 when you receive them. > > > On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts > <[email protected]>wrote: > > > Obed, my question to Thomas was: > > > > One of our I-M223 Project members just received his Geno 2.0 results. He > is > > from the Project's Continental 2a group CTS6433+. When his raw data is > > compared with that of other members he shows PF3514 with A A. All others > > show A G. Ybrowse has PF3514 mutation as A to G. How should I interpret > his > > result? Is he derived and ancestral is actually G or is he ancestral > (back > > mutation) and everyone else is derived? Thanks for any advise, Wayne. > > > > He did not indicate it should be A to C and Ybrowse has A to G. > > > > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> wrote: > > > > > Wayne, > > > > > > Did Thomas explicitly say that the derived value for PF3514 is G, or > > could > > > it be C? My Full Genomes result clearly shows that I have C at this > > > location. I looked at the X and Y sequences in this region and they are > > > indeed very similar, but they do differ at points 17 bases upstream and > > 37 > > > bases downstream of the PF3514 site, which must be enough for Full > > Genomes > > > to separate the Y and X sequences. Full Genomes shows my X sequence to > be > > > identical to the HUGO reference, with A at the PF3514-homologous site. > So > > > Geno 2.0 was clearly in error when they reported me as AG instead of > AC. > > > > > > Although I cannot see their raw data, Full Genomes also reports > several > > > other I1 people to have C at this position. These include another > > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting > to > > > hear what your Full Genomes test showed at the PF3514 site. In > particular > > > I'm wondering if Full Genomes has shown anyone to have G at the PF3514 > > > site. I suppose it's possible that those of us who have C have had a > > second > > > mutation at this site, from G to C. > > > > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > > <[email protected]>wrote: > > > > > > > This is what Thomas had to say about PF3514: > > > > > > > > Everyone in IJ is supposed to be derived. Actually all others have an > > A. > > > It > > > > seems like the region around PF3514 is very similar to > > > > ChrX:91846733..91846902. > > > > > > > > I've made a comparison here: > > > > > > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > > hope this link works for you). > > > > > > > > The X chromosome has also a "A" at this position and the probe on the > > > Geno2 > > > > chip picks them up both. What likely happened is that his ancestors > > were > > > > derived for PF3514, but some X-Y recombination event has wiped that > > > > mutation out at a later time so that it shows the ancestral "A" again > > at > > > > this location. > > > > > > > > ------------------------------- > > > > To unsubscribe from the list, please send an email to > > > > [email protected] 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 > > > [email protected] 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 > > [email protected] 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 > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

I think the Big Y will be done with next-generation sequencing so it should be somewhat comparable to the Full Genomes test. We don't yet know, however, how good the coverage will be. My Full Genomes coverage averaged about 50x; i.e,, an average of about 50 reads for each location looked at, but this varied from about 5 to 100 reads per location. My test found 67 new SNPs and 1 new indel in the "highly reliable" category, and these seemed to be spread out fairly uniformly over a 14 to 15 million base pair region, including locations from 4 to 9.5 million, 13.6 to 23.2 million, and a short stretch around 28.5 million. My raw data BAM file has a size of 12 gb, but the analysis team at Full Genomes talked me through the procedure for downloading it using the wget utility, which turned out to be fairly easy. I can now view my raw data against the human reference sequence using the IGV viewer. On Sat, Jan 4, 2014 at 5:40 PM, Matthew Simonds <[email protected]>wrote: > > >so I have yet to see a next-generation-sequencing sample with G at this > site. > > > Will the Big Y all be done with next-generation-sequencing? I heard that > it will test for 25,000 known SNPs and sequence 10 million base pairs. Will > the testing for the 25,000 known SNPs also be done with > next-generation-sequencing or with a chip? > > Matthew Simonds > > > Date: Sat, 4 Jan 2014 11:52:37 -0600 > > From: [email protected] > > To: [email protected] > > Subject: Re: [yDNAhgI] PF3514 > > > > I see that I had the positions of the mismatches between the HUGO > > reference X and Y sequences slightly off. The mismatch points are 22 > bases > > upstream and 32 bases downstream of the PF3514 site. Also, I looked at > > several I2a samples (HG00360, HG01344, and HG01197) from the 1000 Genomes > > project and they all show C at the site of PF3514, so I have yet to see a > > next-generation-sequencing sample with G at this site. > > > > > > On Sat, Jan 4, 2014 at 3:36 AM, G. Magoon <[email protected]> wrote: > > > > > Hi Wayne, > > > You should be able to find results for PF3514 in the genotyping > ("gtype") > > > report. > > > > > > Nice analysis, Obed! > > > Greg > > > On Jan 4, 2014 3:50 AM, "Wayne R. Roberts" <[email protected]> > > > wrote: > > > > > > > Obed, my samples went to UCLA and unfortunately UCLA results were not > > > > satisfactory. I have sent new samples off to Full Genomes so will > have to > > > > wait longer for results. > > > > > > > > Do you know what result Adam Waalkes received for PF3514? Ken, Aaron > and > > > I > > > > have all his results data but I'm not so sure how to read the raw > data > > > > files. > > > > > > > > > > > > On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> > wrote: > > > > > > > > > Thanks, Wayne. Are you still waiting for your Full Genomes > results? If > > > > so, > > > > > please let us know your result at the site of PF3514 when you > receive > > > > them. > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts > > > > > <[email protected]>wrote: > > > > > > > > > > > Obed, my question to Thomas was: > > > > > > > > > > > > One of our I-M223 Project members just received his Geno 2.0 > results. > > > > He > > > > > is > > > > > > from the Project's Continental 2a group CTS6433+. When his raw > data > > > is > > > > > > compared with that of other members he shows PF3514 with A A. All > > > > others > > > > > > show A G. Ybrowse has PF3514 mutation as A to G. How should I > > > interpret > > > > > his > > > > > > result? Is he derived and ancestral is actually G or is he > ancestral > > > > > (back > > > > > > mutation) and everyone else is derived? Thanks for any advise, > Wayne. > > > > > > > > > > > > He did not indicate it should be A to C and Ybrowse has A to G. > > > > > > > > > > > > > > > > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> > > > wrote: > > > > > > > > > > > > > Wayne, > > > > > > > > > > > > > > Did Thomas explicitly say that the derived value for PF3514 is > G, > > > or > > > > > > could > > > > > > > it be C? My Full Genomes result clearly shows that I have C at > this > > > > > > > location. I looked at the X and Y sequences in this region and > they > > > > are > > > > > > > indeed very similar, but they do differ at points 17 bases > upstream > > > > and > > > > > > 37 > > > > > > > bases downstream of the PF3514 site, which must be enough for > Full > > > > > > Genomes > > > > > > > to separate the Y and X sequences. Full Genomes shows my X > sequence > > > > to > > > > > be > > > > > > > identical to the HUGO reference, with A at the > PF3514-homologous > > > > site. > > > > > So > > > > > > > Geno 2.0 was clearly in error when they reported me as AG > instead > > > of > > > > > AC. > > > > > > > > > > > > > > Although I cannot see their raw data, Full Genomes also > reports > > > > > several > > > > > > > other I1 people to have C at this position. These include > another > > > > > > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be > > > > interesting > > > > > to > > > > > > > hear what your Full Genomes test showed at the PF3514 site. In > > > > > particular > > > > > > > I'm wondering if Full Genomes has shown anyone to have G at the > > > > PF3514 > > > > > > > site. I suppose it's possible that those of us who have C have > had > > > a > > > > > > second > > > > > > > mutation at this site, from G to C. > > > > > > > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > > > > > > <[email protected]>wrote: > > > > > > > > > > > > > > > This is what Thomas had to say about PF3514: > > > > > > > > > > > > > > > > Everyone in IJ is supposed to be derived. Actually all others > > > have > > > > an > > > > > > A. > > > > > > > It > > > > > > > > seems like the region around PF3514 is very similar to > > > > > > > > ChrX:91846733..91846902. > > > > > > > > > > > > > > > > I've made a comparison here: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > > > > > > hope this link works for you). > > > > > > > > > > > > > > > > The X chromosome has also a "A" at this position and the > probe on > > > > the > > > > > > > Geno2 > > > > > > > > chip picks them up both. What likely happened is that his > > > ancestors > > > > > > were > > > > > > > > derived for PF3514, but some X-Y recombination event has > wiped > > > that > > > > > > > > mutation out at a later time so that it shows the ancestral > "A" > > > > again > > > > > > at > > > > > > > > this location. > > > > > > > > > > > > > > > > ------------------------------- > > > > > > > > To unsubscribe from the list, please send an email to > > > > > > > > [email protected] 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 > > > > > > > [email protected] 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 > > > > > > [email protected] 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 > > > > > [email protected] 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 > > > > [email protected] 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 > > > [email protected] 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 > [email protected] 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 > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Obed, my question to Thomas was: One of our I-M223 Project members just received his Geno 2.0 results. He is from the Project's Continental 2a group CTS6433+. When his raw data is compared with that of other members he shows PF3514 with A A. All others show A G. Ybrowse has PF3514 mutation as A to G. How should I interpret his result? Is he derived and ancestral is actually G or is he ancestral (back mutation) and everyone else is derived? Thanks for any advise, Wayne. He did not indicate it should be A to C and Ybrowse has A to G. On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> wrote: > Wayne, > > Did Thomas explicitly say that the derived value for PF3514 is G, or could > it be C? My Full Genomes result clearly shows that I have C at this > location. I looked at the X and Y sequences in this region and they are > indeed very similar, but they do differ at points 17 bases upstream and 37 > bases downstream of the PF3514 site, which must be enough for Full Genomes > to separate the Y and X sequences. Full Genomes shows my X sequence to be > identical to the HUGO reference, with A at the PF3514-homologous site. So > Geno 2.0 was clearly in error when they reported me as AG instead of AC. > > Although I cannot see their raw data, Full Genomes also reports several > other I1 people to have C at this position. These include another > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting to > hear what your Full Genomes test showed at the PF3514 site. In particular > I'm wondering if Full Genomes has shown anyone to have G at the PF3514 > site. I suppose it's possible that those of us who have C have had a second > mutation at this site, from G to C. > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > <[email protected]>wrote: > > > This is what Thomas had to say about PF3514: > > > > Everyone in IJ is supposed to be derived. Actually all others have an A. > It > > seems like the region around PF3514 is very similar to > > ChrX:91846733..91846902. > > > > I've made a comparison here: > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > hope this link works for you). > > > > The X chromosome has also a "A" at this position and the probe on the > Geno2 > > chip picks them up both. What likely happened is that his ancestors were > > derived for PF3514, but some X-Y recombination event has wiped that > > mutation out at a later time so that it shows the ancestral "A" again at > > this location. > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] 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 > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >