For those who want to look at their SNP hierarchy it should look like this in part: S116 AC positive S145 GG positive S474 AG positive S193 AA positive Z2961 AA positive and then the SNPs in the Wilson tree/diagram. However note that you will not see M222 itself: there may be an equivalent or closeby SNP but Dr. Wilson is still double checking this. Iain > From: [email protected] > To: [email protected] > Date: Sat, 16 Nov 2013 07:13:35 +0000 > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > Walter, > > If you ordered the raw version you can download a .txt file whose format I described last month in this post: > > http://archiver.rootsweb.ancestry.com/th/read/DNA-R1B1C7/2013-10/1381923024 > > and that is what we examine. You get it by logging in to your account and clicking the Download button. I can't say for sure that Steve has a downloadable file (yet). If he doesn't he can email [email protected] and they should be able to send it him. > > Iain > > > > > > > Date: Sat, 16 Nov 2013 00:02:57 -0500 > > From: [email protected] > > To: [email protected]; [email protected] > > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > > > Exactly what do your results look like? What is the format? What data > > are you given? How do you access it? Are the designations like S588 > > meaningful such as ATCG (pick one), derived or ancestral), base pair > > indexed, or rs number indexed? > > > > Was the terminal SNP all that you were given back? > > > > I am very interested in running a extended Y-SNP test to compare against > > Steve Lominac, whom I spoke to earlier this evening. But Steve has seen > > no data from his test. Apparently it was run through Sandy Patterson, > > but Steve has not received access to his data file nor his data. > > > > I match Steve 104/111 Y-DNA and we are both SNP tested for R-M222. There > > is a complicated Gordian knot of Freemans, Lominacs, Gills, Sudduth, and > > Nutters all of who are close Y-matches and all of whom have some sort of > > connection to the area between present day Culpepper (formerly > > Fairfield) Culpepper Co, Virginia and Warrenton, Fauquier County > > Virginia. My family tradition is that we are of Irish descent, though > > my earliest known ancestor is a Samuel Freeman b ~1760 +/- whose parents > > and connection to Ireland are unknown at present. > > > > I am most interested in comparing SNPs with Steve who so far seems to be > > ancestral for R-M222, and am considering the Big Y test at FTDNA, which > > seems to be another "pig-in-a-poke" for the moment though it is a > > Y-sequence test and not a chip test, know one knows what data or what > > format a customer will get for his money. I suspect that that test is > > in beta, though FTDNA has not used that language, but they have not been > > forthcoming with any details either. And we know that they recently > > fired the guy, Thomas Krahn, who built their in-house laboratory and > > designed the Big Y test! > > > > I am most interested to see where this all leads and what we can learn > > possibly about our Irish origins. > > > > So what does your data return from BritainsDNA Chromo2 consist of and > > what does it look like? > > > > Thanks, > > > > Walter Freeman > > > > > > On 11/15/2013 2:42 PM, Robert McBride wrote: > > > Just received my Chromo2 results and my terminal snp is s588. > > > > > > Earliest known ancestor Arthur McBride, lived Rampark, Cooley peninsula, died aged 92 in 1879 in Dundalk, County Louth > > > > > > > > > ------------------------------- > > 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

Thanks, Iain. I must have missed your 16 Oct post on the Chromo2 raw file format, or rather was not in the frame of mind at that moment to adsorb that bit of information. I do remember some discussion on this list of form issues with the Chromo2 data and perhaps a bit of an air of disappointment that the data (if as represented below) is not more like what we are used to seeing in a raw file format from 23andMe or FTDNA where there is a reference to the chain position of a SNP and possibly a human genome reference sequence number as well as the SNP call. "S" designations as you show below are not particularly enlightening, possibly because of lack of familiarity with them on my part. To paraphrase, "A SNP by any other name is still a SNP," I suppose except that since much of this is more abstract than your basic rose, it is a bit harder to understand. In the data below, I suppose I am puzzled by the heterozygous calls of S116 and S474. Since there is only one DNA strand and not two, unlike for chromosomes in the autosome, I can understand the homozygous calls for the remaining SNPs shown below as being double letters owing to chip read software programming etc. But why "AC" and why "AG" for S116 and S474? And a further question: How many lines (or SNP calls) of text in the Chromo2 raw file? Tens? Hundreds? Thousands? Walter On 11/16/2013 4:30 AM, Iain Kennedy wrote: > For those who want to look at their SNP hierarchy it should look like this in part: > > S116 AC positive > S145 GG positive > S474 AG positive > S193 AA positive > Z2961 AA positive > > and then the SNPs in the Wilson tree/diagram. However note that you will not see M222 itself: there may be an equivalent or closeby SNP but Dr. Wilson is still double checking this. > > Iain > > From: [email protected] > To: [email protected] > Date: Sat, 16 Nov 2013 07:13:35 +0000 > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > Walter, > > If you ordered the raw version you can download a .txt file whose format I described last month in this post: > > http://archiver.rootsweb.ancestry.com/th/read/DNA-R1B1C7/2013-10/1381923024 > > and that is what we examine. You get it by logging in to your account and clicking the Download button. I can't say for sure that Steve has a downloadable file (yet). If he doesn't he can email [email protected] and they should be able to send it him. > > Iain >

S116 = P312 (R1b1a2a1a2) S146 = L21 (R1b1a2a1a2c) S474 = DF49 (R1b1a2a1a2c1a) S193 = DF23 (R1b1a2a1a2c1a1) They don't seem to have DF13 (S521 -- R1b1a2a1a2c1) Do they give any information regarding the position of the SNP on the Y chromosome? The only way we'll be able to check S588 (and S560 and S561) against public databases (1000 genomes etc.) will be if we know the location of the SNP and the "state change" involved (I'm probably using the wrong term here!) -Paul (DF41+) On Sat, Nov 16, 2013 at 9:30 AM, Iain Kennedy <[email protected]>wrote: > For those who want to look at their SNP hierarchy it should look like this > in part: > > S116 AC positive > S145 GG positive > S474 AG positive > S193 AA positive > Z2961 AA positive > > and then the SNPs in the Wilson tree/diagram. However note that you will > not see M222 itself: there may be an equivalent or closeby SNP but Dr. > Wilson is still double checking this. > > Iain > > > > > > > From: [email protected] > > To: [email protected] > > Date: Sat, 16 Nov 2013 07:13:35 +0000 > > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > > > Walter, > > > > If you ordered the raw version you can download a .txt file whose format > I described last month in this post: > > > > > http://archiver.rootsweb.ancestry.com/th/read/DNA-R1B1C7/2013-10/1381923024 > > > > and that is what we examine. You get it by logging in to your account > and clicking the Download button. I can't say for sure that Steve has a > downloadable file (yet). If he doesn't he can email > [email protected] and they should be able to send it him. > > > > Iain > > > > > > > > > > > > > Date: Sat, 16 Nov 2013 00:02:57 -0500 > > > From: [email protected] > > > To: [email protected]; [email protected] > > > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > > > > > Exactly what do your results look like? What is the format? What data > > > are you given? How do you access it? Are the designations like S588 > > > meaningful such as ATCG (pick one), derived or ancestral), base pair > > > indexed, or rs number indexed? > > > > > > Was the terminal SNP all that you were given back? > > > > > > I am very interested in running a extended Y-SNP test to compare > against > > > Steve Lominac, whom I spoke to earlier this evening. But Steve has > seen > > > no data from his test. Apparently it was run through Sandy Patterson, > > > but Steve has not received access to his data file nor his data. > > > > > > I match Steve 104/111 Y-DNA and we are both SNP tested for R-M222. > There > > > is a complicated Gordian knot of Freemans, Lominacs, Gills, Sudduth, > and > > > Nutters all of who are close Y-matches and all of whom have some sort > of > > > connection to the area between present day Culpepper (formerly > > > Fairfield) Culpepper Co, Virginia and Warrenton, Fauquier County > > > Virginia. My family tradition is that we are of Irish descent, though > > > my earliest known ancestor is a Samuel Freeman b ~1760 +/- whose > parents > > > and connection to Ireland are unknown at present. > > > > > > I am most interested in comparing SNPs with Steve who so far seems to > be > > > ancestral for R-M222, and am considering the Big Y test at FTDNA, which > > > seems to be another "pig-in-a-poke" for the moment though it is a > > > Y-sequence test and not a chip test, know one knows what data or what > > > format a customer will get for his money. I suspect that that test is > > > in beta, though FTDNA has not used that language, but they have not > been > > > forthcoming with any details either. And we know that they recently > > > fired the guy, Thomas Krahn, who built their in-house laboratory and > > > designed the Big Y test! > > > > > > I am most interested to see where this all leads and what we can learn > > > possibly about our Irish origins. > > > > > > So what does your data return from BritainsDNA Chromo2 consist of and > > > what does it look like? > > > > > > Thanks, > > > > > > Walter Freeman > > > > > > > > > On 11/15/2013 2:42 PM, Robert McBride wrote: > > > > Just received my Chromo2 results and my terminal snp is s588. > > > > > > > > Earliest known ancestor Arthur McBride, lived Rampark, Cooley > peninsula, died aged 92 in 1879 in Dundalk, County Louth > > > > > > > > > > > > > ------------------------------- > > > 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 >

Just to clarify that what I was posted was a partial skeleton SNP hierarchy that I reconstructed myself. It is nothing like the full one you could reconstruct from your file if you so desired. But you are right that S521 isn't there. In answer to your second question, I have already posted the all the data columns in the file. :-) cheers Iain > Date: Sat, 16 Nov 2013 12:46:31 +0000 > From: [email protected] > To: [email protected] > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > S116 = P312 (R1b1a2a1a2) > S146 = L21 (R1b1a2a1a2c) > S474 = DF49 (R1b1a2a1a2c1a) > S193 = DF23 (R1b1a2a1a2c1a1) > > They don't seem to have DF13 (S521 -- R1b1a2a1a2c1) > > Do they give any information regarding the position of the SNP on the Y > chromosome? The only way we'll be able to check S588 (and S560 and S561) > against public databases (1000 genomes etc.) will be if we know the > location of the SNP and the "state change" involved (I'm probably using the > wrong term here!) > > -Paul > (DF41+) > > > > On Sat, Nov 16, 2013 at 9:30 AM, Iain Kennedy <[email protected]>wrote: > > > For those who want to look at their SNP hierarchy it should look like this > > in part: > > > > S116 AC positive > > S145 GG positive > > S474 AG positive > > S193 AA positive > > Z2961 AA positive > > > > and then the SNPs in the Wilson tree/diagram. However note that you will > > not see M222 itself: there may be an equivalent or closeby SNP but Dr. > > Wilson is still double checking this. > > > > Iain > > > > > > > > > > > > > From: [email protected] > > > To: [email protected] > > > Date: Sat, 16 Nov 2013 07:13:35 +0000 > > > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > > > > > Walter, > > > > > > If you ordered the raw version you can download a .txt file whose format > > I described last month in this post: > > > > > > > > http://archiver.rootsweb.ancestry.com/th/read/DNA-R1B1C7/2013-10/1381923024 > > > > > > and that is what we examine. You get it by logging in to your account > > and clicking the Download button. I can't say for sure that Steve has a > > downloadable file (yet). If he doesn't he can email > > [email protected] and they should be able to send it him. > > > > > > Iain > > > > > > > > > > > > > > > > > > > Date: Sat, 16 Nov 2013 00:02:57 -0500 > > > > From: [email protected] > > > > To: [email protected]; [email protected] > > > > Subject: Re: [R-M222] Chromo2 Raw Results s588 > > > > > > > > Exactly what do your results look like? What is the format? What data > > > > are you given? How do you access it? Are the designations like S588 > > > > meaningful such as ATCG (pick one), derived or ancestral), base pair > > > > indexed, or rs number indexed? > > > > > > > > Was the terminal SNP all that you were given back? > > > > > > > > I am very interested in running a extended Y-SNP test to compare > > against > > > > Steve Lominac, whom I spoke to earlier this evening. But Steve has > > seen > > > > no data from his test. Apparently it was run through Sandy Patterson, > > > > but Steve has not received access to his data file nor his data. > > > > > > > > I match Steve 104/111 Y-DNA and we are both SNP tested for R-M222. > > There > > > > is a complicated Gordian knot of Freemans, Lominacs, Gills, Sudduth, > > and > > > > Nutters all of who are close Y-matches and all of whom have some sort > > of > > > > connection to the area between present day Culpepper (formerly > > > > Fairfield) Culpepper Co, Virginia and Warrenton, Fauquier County > > > > Virginia. My family tradition is that we are of Irish descent, though > > > > my earliest known ancestor is a Samuel Freeman b ~1760 +/- whose > > parents > > > > and connection to Ireland are unknown at present. > > > > > > > > I am most interested in comparing SNPs with Steve who so far seems to > > be > > > > ancestral for R-M222, and am considering the Big Y test at FTDNA, which > > > > seems to be another "pig-in-a-poke" for the moment though it is a > > > > Y-sequence test and not a chip test, know one knows what data or what > > > > format a customer will get for his money. I suspect that that test is > > > > in beta, though FTDNA has not used that language, but they have not > > been > > > > forthcoming with any details either. And we know that they recently > > > > fired the guy, Thomas Krahn, who built their in-house laboratory and > > > > designed the Big Y test! > > > > > > > > I am most interested to see where this all leads and what we can learn > > > > possibly about our Irish origins. > > > > > > > > So what does your data return from BritainsDNA Chromo2 consist of and > > > > what does it look like? > > > > > > > > Thanks, > > > > > > > > Walter Freeman > > > > > > > > > > > > On 11/15/2013 2:42 PM, Robert McBride wrote: > > > > > Just received my Chromo2 results and my terminal snp is s588. > > > > > > > > > > Earliest known ancestor Arthur McBride, lived Rampark, Cooley > > peninsula, died aged 92 in 1879 in Dundalk, County Louth > > > > > > > > > > > > > > > > > ------------------------------- > > > > 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