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 >

> 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

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