Since you have the other D2 Isles raw data, you can see first hand the clash between you two. Looking at all 9 I can only add: Everyone is CC- for PF6143 except Woods who shows AA+ PF2642 is a misbehaving snp, showing AA for a I1 person, GG- for most everyone, but AG for Woods. How about S7725? Are you in agreement with Woods on that snp? Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: John O'Grady Sent: Saturday, January 11, 2014 9:52 AM To: [email protected] Subject: Re: [yDNAhgI] Chromo2 and Hg I Ken, Full Genomes says that I am PF2642=T+ and PF6143=G-. John O'Grady ------------------------------- 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

Full Genomes doesn't cover the high S SNPs such as S7725, because Wilson hasn't published the positions. My G- for PF6143 agrees with the majority CC- (reverse strand), so PF6143 could split Isles-D. My T+ for PF2642 matches AA+ (reverse strand). I guess we will have to wait for more results. John O'Grady ---------------------------------------- > > Since you have the other D2 Isles raw data, you can see first hand the clash > between you two. Looking at all 9 I can only add: > > Everyone is CC- for PF6143 except Woods who shows AA+ > > PF2642 is a misbehaving snp, showing AA for a I1 person, GG- for most > everyone, but AG for Woods. > > How about S7725? Are you in agreement with Woods on that snp? > > Kenneth Nordtvedt

I have received now 9 Chromo2 raw data files in Haplogroup I, 3 from I1 sector, 3 from I2 M223 sector, and 3 from I2 L161 sector. Every one of the 9 has added a good number of snps to his branch line. See “Tree for L161”, “Chromo2I1work”, and “Chromo2M223work” at website given below for a listing of the new snps found. Some of these snps are of questionable validity but are listed so that we can keep our eye on them as (if) further Chromo2 raw data files are added to our comparisons spreadsheet in the future. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net

Ken, Full Genomes says that I am PF2642=T+ and PF6143=G-. John O'Grady

Diana, By "were due to other Ancestry transfers", I was talking about other people that I matched on Ancestry.com transferring their autosomal from Ancestry.com to FTDNA. I definitely only did the Ancestry --> FTDNA transfer. Robert -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Diana Gale Matthiesen Sent: Friday, January 10, 2014 6:05 PM To: [email protected] Subject: Re: [yDNAhgI] transfer of Ancestry.com autosomal data to FTDNA They would not have given you a FamilyFinder test, unless you had paid for it, so the autosomal DNA matches you are seeing must be based on the Ancestry data you uploaded. You can always check the "Order History" on your member page to be certain what you've ordered. Diana > From: Robert Dozier > Sent: Friday, January 10, 2014 4:51 PM > To: [email protected] > Subject: Re: [yDNAhgI] transfer of Ancestry.com autosomal data to > FTDNA > > Diana, > I only did the autosomal test at Ancestry and had it transferred to FTDNA. > Not sure if the matches I see at FTDNA were due to other Ancestry > transfers or I'd they just did the FTDNA FamilyFinder test. ------------------------------- 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

They would not have given you a FamilyFinder test, unless you had paid for it, so the autosomal DNA matches you are seeing must be based on the Ancestry data you uploaded. You can always check the "Order History" on your member page to be certain what you've ordered. Diana > From: Robert Dozier > Sent: Friday, January 10, 2014 4:51 PM > To: [email protected] > Subject: Re: [yDNAhgI] transfer of Ancestry.com autosomal data to FTDNA > > Diana, > I only did the autosomal test at Ancestry and had it transferred to FTDNA. > Not sure if the matches I see at FTDNA were due to other > Ancestry transfers or I'd they just did the FTDNA FamilyFinder test.

Diana, I only did the autosomal test at Ancestry and had it transferred to FTDNA. Not sure if the matches I see at FTDNA were due to other Ancestry transfers or I'd they just did the FTDNA FamilyFinder test. Robert On Friday, January 10, 2014, Diana Gale Matthiesen wrote: > Robert, > > When you do both, that is, when you take the Family Finder test *and* > transfer > in Ancestry's autosomal data, do they appear separately on your member > page? Or > does FTDNA do some kind of "merge"? (I obviously haven't had any of my > members > do this yet.) > > Diana > > > From: Robert Dozier > > Sent: Friday, January 10, 2014 3:45 PM > > To: [email protected] <javascript:;> > > Subject: Re: [yDNAhgI] transfer of Ancestry.com autosomal data to FTDNA > > > > Bill, > > I did mine a few weeks ago (kit 283178), it did not seem to cause any > > issues. This means no errors were reported back to me. In my > FamilyFinder > > I am seeing some of the same links to others that I had on Ancestry > > > > Robert > > > > On Friday, January 10, 2014, Bill Hawk wrote: > > > > > I arranged to do subject transfer. Downloaded file from Ancestry, and > > > purchased the Family-Finder test. When I look at the unzipped data, it > > > appears that there are formatting errors. The file is tab delimited, > and > > > when the rs number has less than 6 digits, the first tab is missing, > which > > > offsets the columns. I questioned Ancestry about this and the service > > > person said this had been reported before and causes no problems with > data > > > transfer to other companies. Has anybody on the list had experience > with > > > this problem? Does FTDNA recognize and deal with this situation? > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] <javascript:;> with the word > 'unsubscribe' without the quotes in the subject and the body of the message >

Robert, When you do both, that is, when you take the Family Finder test *and* transfer in Ancestry's autosomal data, do they appear separately on your member page? Or does FTDNA do some kind of "merge"? (I obviously haven't had any of my members do this yet.) Diana > From: Robert Dozier > Sent: Friday, January 10, 2014 3:45 PM > To: [email protected] > Subject: Re: [yDNAhgI] transfer of Ancestry.com autosomal data to FTDNA > > Bill, > I did mine a few weeks ago (kit 283178), it did not seem to cause any > issues. This means no errors were reported back to me. In my FamilyFinder > I am seeing some of the same links to others that I had on Ancestry > > Robert > > On Friday, January 10, 2014, Bill Hawk wrote: > > > I arranged to do subject transfer. Downloaded file from Ancestry, and > > purchased the Family-Finder test. When I look at the unzipped data, it > > appears that there are formatting errors. The file is tab delimited, and > > when the rs number has less than 6 digits, the first tab is missing, which > > offsets the columns. I questioned Ancestry about this and the service > > person said this had been reported before and causes no problems with data > > transfer to other companies. Has anybody on the list had experience with > > this problem? Does FTDNA recognize and deal with this situation?

I would recommend also posting this question to the AUTOSOMAL-DNA mailing list: http://lists.rootsweb.ancestry.com/index/other/DNA/AUTOSOMAL-DNA.html The subscribers there have a great deal of experience working with data from both companies (and 23andMe). Diana > From: Bill Hawk > Sent: Friday, January 10, 2014 2:45 PM > To: [email protected] > Subject: [yDNAhgI] transfer of Ancestry.com autosomal data to FTDNA > > I arranged to do subject transfer. Downloaded file from Ancestry, and > purchased the Family-Finder test. When I look at the unzipped data, it appears > that there are formatting errors. The file is tab delimited, and when the rs > number has less than 6 digits, the first tab is missing, which offsets the > columns. I questioned Ancestry about this and the service person said this had > been reported before and causes no problems with data transfer to other > companies. Has anybody on the list had experience with this problem? Does > FTDNA recognize and deal with this situation?

Bill, I did mine a few weeks ago (kit 283178), it did not seem to cause any issues. This means no errors were reported back to me. In my FamilyFinder I am seeing some of the same links to others that I had on Ancestry Robert On Friday, January 10, 2014, Bill Hawk wrote: > I arranged to do subject transfer. Downloaded file from Ancestry, and > purchased the Family-Finder test. When I look at the unzipped data, it > appears that there are formatting errors. The file is tab delimited, and > when the rs number has less than 6 digits, the first tab is missing, which > offsets the columns. I questioned Ancestry about this and the service > person said this had been reported before and causes no problems with data > transfer to other companies. Has anybody on the list had experience with > this problem? Does FTDNA recognize and deal with this situation? > > Bill > kit #117095 > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] <javascript:;> with the word > 'unsubscribe' without the quotes in the subject and the body of the message >

In regard to the recent discussion about the apparent discrepancy between SNPs PF3514 and FGC2408 at position 5578919 of the Y, I looked further at my Full Genomes results to see which named SNPs show the highest number of discrepancies with my FGC results. The winner hands down, with 57 discrepancies, was the PF series of SNPs, but the discrepant PF SNPs are all in only 2 PF number regions, from PF3503 to PF3564, and from PF5998 to PF6094. There were only 2 discordant SNPs among the F series, 1 for the Z series, and none for the CTS series. Some of these discrepancies could be due to second mutations at the same site, but I think most are due to simple errors. I found these by searching for "site of PF" (or "site of F", etc.) in my HaplogroupCompare file, which includes all of my SNPs which differ from the HUGO reference. So it appears that whoever entered the data in the original reference for the PF SNPs in the above regions was a little sloppy.

I arranged to do subject transfer. Downloaded file from Ancestry, and purchased the Family-Finder test. When I look at the unzipped data, it appears that there are formatting errors. The file is tab delimited, and when the rs number has less than 6 digits, the first tab is missing, which offsets the columns. I questioned Ancestry about this and the service person said this had been reported before and causes no problems with data transfer to other companies. Has anybody on the list had experience with this problem? Does FTDNA recognize and deal with this situation? Bill kit #117095

I should have read this message before posting comment about Motala2 on the other message. On Thu, Jan 9, 2014 at 7:47 AM, Kenneth Nordtvedt <[email protected]>wrote: > And I made a @#$%% typo. Motala2 is M253- of course. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Kenneth Nordtvedt > Sent: Wednesday, January 08, 2014 2:22 PM > To: [email protected] > Subject: [yDNAhgI] phyloequivalent ysnps > > In my recent message about ancient haplogroup I in Europe I forgot to > include a comment on phyloequivalent snps. Here it is. > > So you can see the importance in Tree building of keeping track of the full > list of phyloequivalent snps for every branch segment of the Tree, > especially as the branch segments are further upstream. > > As the business of recovering the most complete ydna as possible for very > old bones continues, and we want to extract information from those > reconstructed y chromosomes, necessarily the reconstructions will be > incomplete to various degrees depending on soils and climate conditions, > etc. Not all snp sites will be readable. So as complete as possible a > list > of phyloequivalent snps in our Tree gives the most number of alternative > sites to read in the reconstructed ydna of the ancients. This will allow > for more information extracted from that ancient dna for better location of > the ancient dna in the Tree. > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > 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 >

Kenneth, That is very interesting. Could you confirm however that Motala2 was M253+ as you said or if this was a typo and he is M253-. Thanks On Thu, Jan 9, 2014 at 7:12 AM, Kenneth Nordtvedt <[email protected]>wrote: > Here’s an update on what has recently been learned about haplogroup I ydna > in ancient Europe. Bones of several males from 8000 b.p. were examined for > their dna: Loschbour was from a Luxuemberg site, four male dna Motala > 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems > not to be confirmed haplogroup I, but his true haplogroup is still > unidentified though thought Q for awhile. Their ydna analysis of these > ancient males is discussed in depth in the paper “Ancient human genomes > suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of > phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, > L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, > CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades > or from the L621 “Dinaric” clade were found derived for ALL of these 12 > ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these > ancient dna samples. They took their snps to test from ISOGG list, and as > we know that list always lags present knowledge because of the procedure of > inclusion into their list. The ancient dna samples are not necessarily > readable on any given snp site, so it is important to have that ancient dna > tested on alternative sites of equivalence if unreadable on any particular > site. So I sent the 10 snp sites listed above for which they did not test > to authors of the cited paper. They very kindly looked up the allele > values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, > CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other > five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly > matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching > Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first > three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line > of the I Tree which is today probably extinct or severely tiny in present > population. It splits the 12 snps into ancestrals and deriveds. See > “Tree and Map for haplogroup I” for position of this new branch of the > tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 > samples using the rich catalog of well placed ysnps that has resulted from > Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about > Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are > haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He > could be anything in I2...... and could be a new ancient branch on the > ancestral I1 line which branched off prior to P40. That’s a time range of > 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have > branched off of the ancestral I1 line anytime before M253, and Motala still > has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 > generated rich lists of phylogenetically equivalent snps for many of the > key branch segments of the I tree. Motala2 and Motala9 could conceivably > be placed fairly well in the haplogroup I tree, giving us much better > incite into presence of our haplogroup in northern Europe 8000 years ago. > I have sent several sets of the confirmed phylogenetically equivalent snp > lists to them and hopefully they will see if they are readable for Motala2 > and Motala9. > > What I have not put together yet, waiting to see if they will use it or > that Motala2 and Motala9 are not confirmed to be part of I2....., is the > very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 > snps). Since that branch line segment is so long, 22000 years ago up to > 4500 years ago, the list of well confirmed equivalent snps is probably > presently approaching 100 in number. If Motala2 or Motala9 are confirmed > I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient > dna samples from a complete use of their full genome measurements plus the > hobby community’s most up to date list of well confirmed and well placed > ysnps. > I hope they will continue to work with us as they did on the initial set > of ysnps equivalent to M423 and L178 which produced such informative > results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited > paper concluded, then a complete list of phylogenetically equivalent snps > to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > 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

It was a typo: Ken: And I made a @#$%% typo. Motala2 is M253- of course. > Date: Thu, 9 Jan 2014 08:14:38 +1000 > From: [email protected] > To: [email protected] > Subject: Re: [yDNAhgI] Update on Ancient I in Europe > > Kenneth, > > That is very interesting. > > Could you confirm however that Motala2 was M253+ as you said or if this was > a typo and he is M253-. > > Thanks > > > On Thu, Jan 9, 2014 at 7:12 AM, Kenneth Nordtvedt <[email protected]>wrote: > > > Here’s an update on what has recently been learned about haplogroup I ydna > > in ancient Europe. Bones of several males from 8000 b.p. were examined for > > their dna: Loschbour was from a Luxuemberg site, four male dna Motala > > 2,3,9,12 > > were from a Swedish site. Another male from Swedish site, Motala6, seems > > not to be confirmed haplogroup I, but his true haplogroup is still > > unidentified though thought Q for awhile. Their ydna analysis of these > > ancient males is discussed in depth in the paper “Ancient human genomes > > suggest three ancestral populations for presentday Europeans”. > > > > As of a month ago, the hobby community had collected a number of > > phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, > > L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, > > CTS1293, CTS11030. > > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades > > or from the L621 “Dinaric” clade were found derived for ALL of these 12 > > ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > > > In the cited paper, however, only L178 and M423 were tested on these > > ancient dna samples. They took their snps to test from ISOGG list, and as > > we know that list always lags present knowledge because of the procedure of > > inclusion into their list. The ancient dna samples are not necessarily > > readable on any given snp site, so it is important to have that ancient dna > > tested on alternative sites of equivalence if unreadable on any particular > > site. So I sent the 10 snp sites listed above for which they did not test > > to authors of the cited paper. They very kindly looked up the allele > > values for the additional snps which could be read. > > > > Loschbour was readable for all 12 snps with results: derived for CTS8239, > > CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other > > five snps including L1224. > > > > Motala12 was readable for 9 of the 12 snps with results which exactly > > matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > > > Motala3 was readable for only 3 of the 12 snps with results matching > > Loschbour: CTS7218+, CTS176+, CTS1293+ > > > > Motala2 was readable for only 1 of the 12 snps and disagreed with first > > three dna samples, being CTS1293- > > > > Motala9 was not readable for any of the 12 snps. > > > > Loschbour and Motala12 (and probably Motala3) establish a new branch line > > of the I Tree which is today probably extinct or severely tiny in present > > population. It splits the 12 snps into ancestrals and deriveds. See > > “Tree and Map for haplogroup I” for position of this new branch of the > > tree. > > > > So we concentrate on what we might further learn about Motala2 and Motala9 > > samples using the rich catalog of well placed ysnps that has resulted from > > Geno2 and other products done by hobbyists. > > > > All we know about Motala9 is that he is P38+ but P40-. All we know about > > Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are > > haplogroup I, but that’s about all we know. > > Motala9 could be most anything within haplogroup I except a modern I1. He > > could be anything in I2...... and could be a new ancient branch on the > > ancestral I1 line which branched off prior to P40. That’s a time range of > > 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have > > branched off of the ancestral I1 line anytime before M253, and Motala still > > has much of I2...... for his location. > > > > So there is much work that authors of this paper can do using our Geno2 > > generated rich lists of phylogenetically equivalent snps for many of the > > key branch segments of the I tree. Motala2 and Motala9 could conceivably > > be placed fairly well in the haplogroup I tree, giving us much better > > incite into presence of our haplogroup in northern Europe 8000 years ago. > > I have sent several sets of the confirmed phylogenetically equivalent snp > > lists to them and hopefully they will see if they are readable for Motala2 > > and Motala9. > > > > What I have not put together yet, waiting to see if they will use it or > > that Motala2 and Motala9 are not confirmed to be part of I2....., is the > > very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 > > snps). Since that branch line segment is so long, 22000 years ago up to > > 4500 years ago, the list of well confirmed equivalent snps is probably > > presently approaching 100 in number. If Motala2 or Motala9 are confirmed > > I2..... then no sense checking them on all those I1 snps. > > > > So there could be much more of value to be extracted from these ancient > > dna samples from a complete use of their full genome measurements plus the > > hobby community’s most up to date list of well confirmed and well placed > > ysnps. > > I hope they will continue to work with us as they did on the initial set > > of ysnps equivalent to M423 and L178 which produced such informative > > results. > > > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited > > paper concluded, then a complete list of phylogenetically equivalent snps > > to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > > > > > > > > > > > Kenneth Nordtvedt > > > > Haplogroup I Clade Modalities and Trees at: > > http://knordtvedt.home.bresnan.net > > > > > > ------------------------------- > > 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

>the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps)When we talk about SNPs being phyloequivalent, does that only mean that they are phyloequivalent for modern I1? For example, if all modern I1s are M253+ P40+ and both SNPs can define haplogroup I1, are we likely to find some remains eventually that are perhaps P40+ but M253- and represent some intermediate stage? Matthew Simonds > From: [email protected] > To: [email protected] > Date: Wed, 8 Jan 2014 14:12:40 -0700 > Subject: [yDNAhgI] Update on Ancient I in Europe > > Here’s an update on what has recently been learned about haplogroup I ydna in ancient Europe. Bones of several males from 8000 b.p. were examined for their dna: Loschbour was from a Luxuemberg site, four male dna Motala 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems not to be confirmed haplogroup I, but his true haplogroup is still unidentified though thought Q for awhile. Their ydna analysis of these ancient males is discussed in depth in the paper “Ancient human genomes suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades or from the L621 “Dinaric” clade were found derived for ALL of these 12 ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these ancient dna samples. They took their snps to test from ISOGG list, and as we know that list always lags present knowledge because of the procedure of inclusion into their list. The ancient dna samples are not necessarily readable on any given snp site, so it is important to have that ancient dna tested on alternative sites of equivalence if unreadable on any particular site. So I sent the 10 snp sites listed above for which they did not test to authors of the cited paper. They very kindly looked up the allele values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line of the I Tree which is today probably extinct or severely tiny in present population. It splits the 12 snps into ancestrals and deriveds. See “Tree and Map for haplogroup I” for position of this new branch of the tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 samples using the rich catalog of well placed ysnps that has resulted from Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He could be anything in I2...... and could be a new ancient branch on the ancestral I1 line which branched off prior to P40. That’s a time range of 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have branched off of the ancestral I1 line anytime before M253, and Motala still has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 generated rich lists of phylogenetically equivalent snps for many of the key branch segments of the I tree. Motala2 and Motala9 could conceivably be placed fairly well in the haplogroup I tree, giving us much better incite into presence of our haplogroup in northern Europe 8000 years ago. I have sent several sets of the confirmed phylogenetically equivalent snp lists to them and hopefully they will see if they are readable for Motala2 and Motala9. > > What I have not put together yet, waiting to see if they will use it or that Motala2 and Motala9 are not confirmed to be part of I2....., is the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps). Since that branch line segment is so long, 22000 years ago up to 4500 years ago, the list of well confirmed equivalent snps is probably presently approaching 100 in number. If Motala2 or Motala9 are confirmed I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient dna samples from a complete use of their full genome measurements plus the hobby community’s most up to date list of well confirmed and well placed ysnps. > I hope they will continue to work with us as they did on the initial set of ysnps equivalent to M423 and L178 which produced such informative results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited paper concluded, then a complete list of phylogenetically equivalent snps to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > 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, I gather you are talking about the Full Genomes results that are presented in the "variantCompare" and "haplogroupCompare" reports. First some background: There are essentially two different types of bioinformatic analysis that are traditionally used to interpret next-gen sequencing results. The first, which might be called "genotyping", involves looking at sites of known variation (e.g. M253) and figuring out what is the allele at that site; this is what is done by the gtype report. The second goes by the name of "variant discovery", "variant identification", or "variant calling" ("variant" may be also replaced by "SNP" to refer to that particular type of variant which is most commonly discussed); here, the idea is to identify differences from the reference human genome without any *a priori* knowledge about what these variations are or where they will be found (though often the variants that are found may be identified as corresponding to known variants after the fact); this latter process is the basis for the "variantCompare" and "haplogroupCompare" reports. With that as background, I'll try to address your question about the "Reliability flag", which is indicated by varying number of asterisks (*), with higher number of * corresponding to less reliable variants that are more likely to be false-positives. The goal here is to avoid the identification of significant numbers of spurious, false-positive variants, as next-gen sequencing methods are prone to doing. Certain regions of chrY are more prone to these issues than others. A number of factors are taken into consideration when "binning" the variants by reliability. The reliability indicator provides a rough indication of the likelihood of a genuine variant for purposes of novel variant identification (rather than probability of a particular genotype). So, certain well-known variants may be classified as ** or *** when in fact underlying results are solid (and further details can be seen on the gtype report). The reliability flag is more useful for variants that have not been extensively studied (e.g. confirmed by conventional Sanger sequencing). The reliability reporting system has been set up such that variants with no asterisk or one asterisk may be considered "high reliability", and these are the ones to focus on initially. Some of the ** variants may also prove to be useful...the call pattern for other samples in the haplogroupCompare report can be a useful guideline (if the call pattern makes sense, and is consistent with other results, then there is a good chance the variant is genuine). Most of the *** variants are probably false positives. Regarding your question independence of reads, part of the analysis that is performed involves identification of potential "PCR duplicates". This is related to your point about reading the same thing over and over, which, as you note, can bias the results. Reads identified by the computer as PCR duplicates are marked as such and this can be taken into account in subsequent analyses to avoid biases in the results. Hope this helps, Greg On Wed, Jan 8, 2014 at 8:13 PM, Kenneth Nordtvedt <[email protected]>wrote: > The list of I phyloequivalents could be very useful. Thank you for > suppling > it. > > Could you explain the no asterix, one asterix. two ...... rating system. > > Everything I have seen is technical goobly gook talk to me. Can it be > reexplained in plain English. "Number of reads" by itself means nothing by > itself to me. Is the same piece of lab guuu being read over and over? > That would be sort of a waste of time; wouldn't you get the same result if > reading the same stuff over and over? If number of reads is to mean > anything important it must be independent reads on different stuff which > under some model or theory should be yielding the same output. > "Independence" of the operations is key. > > So please; how does the asterix rating system really operate, and how do > they lead to the percentages, whatever they mean. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > >

Tx Bernie! > From: [email protected] > Date: Wed, 8 Jan 2014 14:23:07 -0500 > To: [email protected] > Subject: Re: [yDNAhgI] I2a2b and PF3514 > > I think Geno 2.0 has recalibrated/fixed PF3514 recently. I have multiple > PF3514=A,A in I-P37.2 since November, before that they were almost all A G. > > Bernie > > ------------------------------- > 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

Hi all, Today I received a I-L38 (I2a2b) Geno2.0 raw data file. It has a curious PF3514 = A,A According the chromosome browser A=ancestral and G=derived. All other I-L38 Geno2.0 samples have a PF3514=A,G. Also M23 and L161 samples have PF3514=A,G. How to interprete this curious PF3514 = A,A? Is it a miscall - or do all the other samples have a PF3514 miscall? Best, Hans

Just a reminder--the one "Dinaric-cousin" person from southern Poland is L147-, so knowing that HG00360 is L621+ and L147+ is pretty good evidence that he is a normal Dinaric. See this tree: http://i2aproject.blogspot.com/2013/12/i-p372-tree-showing-main-dinaric.html Bernie On Wed, Jan 8, 2014 at 7:42 PM, John O'Grady <[email protected]>wrote: > YFull says that HG00360 is L621: > > http://www.yfull.com/tree/I2a1b3/ > > John O'Grady > > > > > Greg, I see this note about HG00360 at the spreadsheet: > > "I2a-M423, L147+, L69.2+, P41/M359-; originally listed as L621+, but > GregRM > > can't find any evidence of this in mapped sequence data" > > > > Still I think it's very likely that he is L621+ and a normal Dinaric > (this > > occurrence L147 is supposed to be downstream of L621 after all). > > > > Bernie > > ------------------------------- > 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 read every email but I'm not always able to respond immediately. If you think you've been waiting too long for a reply, please, email me again at [email protected]