Dear Tim, thank you. In the event of a possible genotyping error by the testing company resulting in a failure to call the intervening segment an HIR, how would one confirm that? My assumption is that the Download Raw Data option in FTDNA which yields a zip file can be accessed and one needs to actually look at the alleles for each SNP. Is that correct? I have never tried this. When you unzip the file, does it generate a single Excel file that you can open to see the reported alleles? Barton On Wed, Oct 09, 2013 at 01:29 AM, Tim Janzen wrote: > Dear Barton, > It is certainly reasonable to believe that both of these HIRs > (presumably IBD segments) can be traced back to the known shared > ancestors > at the 5th cousin level of relationship. I have an example in my > family of > two fifth cousins sharing 33 cMs in two segments. However, you should > always keep in mind the possibility that one of the two segments comes > from > a different shared ancestor than the known shared ancestors at the 5th > cousin level of relationship. My mom recently had a match at 23andMe > that > shares two HIRs with her. I had previously mapped one of those > segments to > my mom's father and the other to my mom's maternal grandfather using > data > from first and second cousins. When one is dealing with people from > endogamous populations then one has to be particularly alert for > situations > such as this where one shared segment came from one shared ancestor > and the > other shared segment came from a different shared ancestor. This is > where > your chromosome map is crucial. If you have tested a fair number of > first, > second, and third cousins then you will have a good idea whether two > segments you share with a 5th cousin may have came from the same > shared > ancestor if you have previously mapped the segments in question. The > location of shared segments within the genome is entirely random. You > can > certainly have crossovers that split a shared segment such as what > appears > to be the case in this situation. I recently had a similar situation > in my > family's results at 23andMe. However, you should also keep in mind > that one > or more genotyping errors in the section between 30027010 and 33868089 > could > be preventing the company from calling this particular section an HIR. > In > such cases, the entire HIR (from 25354798 to 47167537) is actually a > shared > IBD segment. > Sincerely, > Tim Janzen > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Barton Lewis > Sent: Tuesday, October 08, 2013 7:51 PM > To: autosomal-dna@rootsweb.com > Subject: [AUTOSOMAL-DNA] Same or different segment? > > My aunt matches her fifth cousin on chr 17 as follows: > > 25354798 30027010 7.84 1249 33868089 47167537 12.67 2900 > Is it likely these 2 sections are from the same ancestor? How close do > segments have to be to make it likely they are from the same ancestor? > What > accounts for a section being "broken up" in this way? What's a good > layman's way of understanding "how big is big" when talking about > these > kinds of break up on a chromosome? > > Barton > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please > see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Barton If you can upload to GEDmatch, you can see the chromosomes compared in pretty good detail. You'd look at the position in question and see if it could be considered two adjoining, smaller segments that some algorithms call one larger segment, some don't. I've run across this several times. Jim - Sent from my iPhone - FaceTime! On Oct 9, 2013, at 3:23 PM, BARTON LEWIS <bartonlewis@optonline.net> wrote: > Dear Tim, thank you. In the event of a possible genotyping error by the > testing company resulting in a failure to call the intervening segment > an HIR, how would one confirm that? My assumption is that the Download > Raw Data option in FTDNA which yields a zip file can be accessed and one > needs to actually look at the alleles for each SNP. Is that correct? I > have never tried this. When you unzip the file, does it generate a > single Excel file that you can open to see the reported alleles? > > Barton > > > On Wed, Oct 09, 2013 at 01:29 AM, Tim Janzen wrote: > >> Dear Barton, >> It is certainly reasonable to believe that both of these HIRs >> (presumably IBD segments) can be traced back to the known shared >> ancestors >> at the 5th cousin level of relationship. I have an example in my >> family of >> two fifth cousins sharing 33 cMs in two segments. However, you should >> always keep in mind the possibility that one of the two segments comes >> from >> a different shared ancestor than the known shared ancestors at the 5th >> cousin level of relationship. My mom recently had a match at 23andMe >> that >> shares two HIRs with her. I had previously mapped one of those >> segments to >> my mom's father and the other to my mom's maternal grandfather using >> data >> from first and second cousins. When one is dealing with people from >> endogamous populations then one has to be particularly alert for >> situations >> such as this where one shared segment came from one shared ancestor >> and the >> other shared segment came from a different shared ancestor. This is >> where >> your chromosome map is crucial. If you have tested a fair number of >> first, >> second, and third cousins then you will have a good idea whether two >> segments you share with a 5th cousin may have came from the same >> shared >> ancestor if you have previously mapped the segments in question. The >> location of shared segments within the genome is entirely random. You >> can >> certainly have crossovers that split a shared segment such as what >> appears >> to be the case in this situation. I recently had a similar situation >> in my >> family's results at 23andMe. However, you should also keep in mind >> that one >> or more genotyping errors in the section between 30027010 and 33868089 >> could >> be preventing the company from calling this particular section an HIR. >> In >> such cases, the entire HIR (from 25354798 to 47167537) is actually a >> shared >> IBD segment. >> Sincerely, >> Tim Janzen >> >>

Dear Barton, You need to open the zipped files for the people in question and review the raw data files. The raw data files are .csv files, which can be readily opened in Excel. It can be difficult to determine if there was a genotyping error. You first have to compare the raw SNP data for the people in question to see where the SNPs are not consistent with a shared IBD segment. This can readily be done in Excel either by visually reviewing the data or writing a small formula that does that for you. Once you have narrowed down the SNPs that are not consistent with a shared IBD segment you need to look at the total number of these SNPs for the region in question. If there are only one or two SNPs that are discrepant in a relatively long run of 2000 SNPs or so, then there could be a genotyping error. However, if you find that there are 5 to 10 or more discrepant SNPs in a run of 2000 SNPs, then it is much more likely that the region in question is not an IBD segment. You can then review the data from parents or children of the people in question to see if the data for those particular discrepant SNPs is consistent with the data you have from the parents or children of the people in question. In my experience there are about 200 to 300 genotyping errors in the raw data files of a 2 parent/1 child trio. Sincerely, Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of BARTON LEWIS Sent: Wednesday, October 09, 2013 7:24 AM To: autosomal-dna@rootsweb.com Cc: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Same or different segment? Dear Tim, thank you. In the event of a possible genotyping error by the testing company resulting in a failure to call the intervening segment an HIR, how would one confirm that? My assumption is that the Download Raw Data option in FTDNA which yields a zip file can be accessed and one needs to actually look at the alleles for each SNP. Is that correct? I have never tried this. When you unzip the file, does it generate a single Excel file that you can open to see the reported alleles? Barton

Thank you, Tim. Barton On Thu, Oct 10, 2013 at 08:10 PM, Tim Janzen wrote: > Dear Barton, > You need to open the zipped files for the people in question and > review the raw data files. The raw data files are .csv files, which > can be > readily opened in Excel. It can be difficult to determine if there was > a > genotyping error. You first have to compare the raw SNP data for the > people > in question to see where the SNPs are not consistent with a shared IBD > segment. This can readily be done in Excel either by visually > reviewing the > data or writing a small formula that does that for you. Once you have > narrowed down the SNPs that are not consistent with a shared IBD > segment you > need to look at the total number of these SNPs for the region in > question. > If there are only one or two SNPs that are discrepant in a relatively > long > run of 2000 SNPs or so, then there could be a genotyping error. > However, if > you find that there are 5 to 10 or more discrepant SNPs in a run of > 2000 > SNPs, then it is much more likely that the region in question is not > an IBD > segment. You can then review the data from parents or children of the > people in question to see if the data for those particular discrepant > SNPs > is consistent with the data you have from the parents or children of > the > people in question. In my experience there are about 200 to 300 > genotyping > errors in the raw data files of a 2 parent/1 child trio. > Sincerely, > Tim Janzen > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of BARTON LEWIS > Sent: Wednesday, October 09, 2013 7:24 AM > To: autosomal-dna@rootsweb.com > Cc: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Same or different segment? > > Dear Tim, thank you. In the event of a possible genotyping error by > the testing company resulting in a failure to call the intervening > segment an HIR, how would one confirm that? My assumption is that the > Download Raw Data option in FTDNA which yields a zip file can be > accessed and one needs to actually look at the alleles for each SNP. > Is that correct? I have never tried this. When you unzip the file, > does it generate a single Excel file that you can open to see the > reported alleles? > > Barton > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please > see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >