David, this is no mystery, you yourself present the explanation. Ancestry has LESS SNPs along the pileup - 460 compared to 612 of 23andMe. This means you threshold of 5cM and !! 500 SNPs !! is too strict for pile-up only match of the A kit. It has to be supported by at least 40 cumulative SNP of IBS regions on both sides of the pileup. Whereas 23andMe can easily satisfy the 500 SNP threshold you set for your experiments. Setting the threshold to 400 SNPs should bring the number of pile-up matches for A kit up, while setting it to 700 SNPs should bring it down for the M kit to verify this theory. Best regards, Kuba On Wed, Jan 6, 2016 at 9:37 PM, David Schroeder via < genealogy-dna@rootsweb.com> wrote: > For comparison for the matches I had on Chromosome = '15' and (POS > > 23976155 AND POS < 25855576) My pileup region > > +-----------+---------+ > | Fixed ANC | AVG(CM) | > +-----------+---------+ > | 119 | 10.2 | > +-----------+---------+ > +----------+---------+ > | Orig ANC | AVG(CM) | > +----------+---------+ > | 150 | 10.0 | > +----------+---------+ > +---------------+---------+ > | Fixed 23andme | AVG(CM) | > +---------------+---------+ > | 442 | 8.6 | > +---------------+---------+ > +--------------+---------+ > | Orig 23andme | AVG(CM) | > +--------------+---------+ > | 556 | 8.3 | > +--------------+---------+ > > It is a mystery to me why 23andme generated more matches in my pileup > region. > > David Schroeder > > -----Original Message----- > From: David Schroeder [mailto:dschroed991@sbcglobal.net] > Sent: Wednesday, January 6, 2016 2:18 PM > To: 'ahnen@awest.de'; 'genealogy-dna@rootsweb.com' > Subject: RE: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA > > Sorry about the sea of information. There were so many comparisons, and > each > one had surprising results. > > I think I can say at least 25% of my matches coming from 23andme were from > a > Pile-up on Chromosome 15: POS > 23976155 and POS < 25855576). > > I looked at the two kits, Ancestry checks for 460 RSIDs in this range of > positions. 23andme checks for 602. The pileups for Ancestry are much less > than 23andme. Ancestry only had 12 no-calls in this region, 23andme only > had > 17. I don't know why there were hundreds more matches in this range for > 23andme compared to Ancestry. > > David > > > > -----Original Message----- > From: ahnen@awest.de [mailto:ahnen@awest.de] > Sent: Wednesday, January 6, 2016 11:09 AM > To: David Schroeder; genealogy-dna@rootsweb.com > Subject: Re: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA > > David, > > A summary on the last comparisons would be fine. I've got lost in the many > tables which despite your wonderful effort are still hard to read in plain > email format. > > Great analysis! > > Andreas > > > ------------------------------- > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Kuba, Please help me understand. Using the ISOGG Chart, “Ratio of Observed to Expected IBD”, a.k.a. pileup regions, I incorporated the position values into my query to see how the matches change from the original kit vs the fixed kit: Using ISOGG values: 23andme Original Kit: 426 matches vs 23andme fixed kit: 405 matches (these are matches that occur only in the ISOGG pile-up regions) I have a large number of matches on chromosome 15 that fall just beyond the ISOGG position of 25145260. I increased the start position for the pileup region to include up to 25671399 and got these numbers: 23andme Original Kit: 671 matches vs 541 matches in the 23andme fixed kit. In either comparison there was a significant reduction for the 23andme fixed kit. Running the same query with ancestry with the expanded position range on chromosome 15: Ancestry Original: 184 vs Ancestry Fixed: 230 matches. This seems to go along with what you are saying: More SNPs enable more matches in the pile-up regions. But, I suppose that the more numerous SNPs in the 23andme fixed kit began to reduce that number? Apparently you have insight into the calculation. Please explain, "It has to be supported by at least 40 cumulative SNP of IBS regions on both sides of the pileup"? Thank you, David Schroeder From: gkg.the.lame@gmail.com [mailto:gkg.the.lame@gmail.com] On Behalf Of Kuba Krchak Sent: Thursday, January 7, 2016 1:35 AM To: David Schroeder; genealogy-dna@rootsweb.com Cc: Andreas West Subject: Re: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA David, this is no mystery, you yourself present the explanation. Ancestry has LESS SNPs along the pileup - 460 compared to 612 of 23andMe. This means you threshold of 5cM and !! 500 SNPs !! is too strict for pile-up only match of the A kit. It has to be supported by at least 40 cumulative SNP of IBS regions on both sides of the pileup. Whereas 23andMe can easily satisfy the 500 SNP threshold you set for your experiments. Setting the threshold to 400 SNPs should bring the number of pile-up matches for A kit up, while setting it to 700 SNPs should bring it down for the M kit to verify this theory. Best regards, Kuba On Wed, Jan 6, 2016 at 9:37 PM, David Schroeder via <genealogy-dna@rootsweb.com> wrote: For comparison for the matches I had on Chromosome = '15' and (POS > 23976155 AND POS < 25855576) My pileup region +-----------+---------+ | Fixed ANC | AVG(CM) | +-----------+---------+ | 119 | 10.2 | +-----------+---------+ +----------+---------+ | Orig ANC | AVG(CM) | +----------+---------+ | 150 | 10.0 | +----------+---------+ +---------------+---------+ | Fixed 23andme | AVG(CM) | +---------------+---------+ | 442 | 8.6 | +---------------+---------+ +--------------+---------+ | Orig 23andme | AVG(CM) | +--------------+---------+ | 556 | 8.3 | +--------------+---------+ It is a mystery to me why 23andme generated more matches in my pileup region. David Schroeder -----Original Message----- From: David Schroeder [mailto:dschroed991@sbcglobal.net] Sent: Wednesday, January 6, 2016 2:18 PM To: 'ahnen@awest.de'; 'genealogy-dna@rootsweb.com' Subject: RE: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA Sorry about the sea of information. There were so many comparisons, and each one had surprising results. I think I can say at least 25% of my matches coming from 23andme were from a Pile-up on Chromosome 15: POS > 23976155 and POS < 25855576). I looked at the two kits, Ancestry checks for 460 RSIDs in this range of positions. 23andme checks for 602. The pileups for Ancestry are much less than 23andme. Ancestry only had 12 no-calls in this region, 23andme only had 17. I don't know why there were hundreds more matches in this range for 23andme compared to Ancestry. David -----Original Message----- From: ahnen@awest.de [mailto:ahnen@awest.de] Sent: Wednesday, January 6, 2016 11:09 AM To: David Schroeder; genealogy-dna@rootsweb.com Subject: Re: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA David, A summary on the last comparisons would be fine. I've got lost in the many tables which despite your wonderful effort are still hard to read in plain email format. Great analysis! Andreas ------------------------------- To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

David I have not played with with what you are working on but since you mention a shift in the segment start point: Are you sure you are comparing raw Data and files generated using the same Build number. Some start and stop points shift when using Build 36 data Vs. Build 37 data. The Build is the mapping schematic that is used to reassemble the test results into the raw data file. RPaine -----Original Message----- From: David Schroeder via Sent: Friday, January 8, 2016 1:17 PM To: 'Kuba Krchak' ; genealogy-dna@rootsweb.com Subject: Re: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA Kuba, Please help me understand. Using the ISOGG Chart, “Ratio of Observed to Expected IBD”, a.k.a. pileup regions, I incorporated the position values into my query to see how the matches change from the original kit vs the fixed kit: Using ISOGG values: 23andme Original Kit: 426 matches vs 23andme fixed kit: 405 matches (these are matches that occur only in the ISOGG pile-up regions) I have a large number of matches on chromosome 15 that fall just beyond the ISOGG position of 25145260. I increased the start position for the pileup region to include up to 25671399 and got these numbers: 23andme Original Kit: 671 matches vs 541 matches in the 23andme fixed kit. In either comparison there was a significant reduction for the 23andme fixed kit. Running the same query with ancestry with the expanded position range on chromosome 15: Ancestry Original: 184 vs Ancestry Fixed: 230 matches. This seems to go along with what you are saying: More SNPs enable more matches in the pile-up regions. But, I suppose that the more numerous SNPs in the 23andme fixed kit began to reduce that number? Apparently you have insight into the calculation. Please explain, "It has to be supported by at least 40 cumulative SNP of IBS regions on both sides of the pileup"? Thank you, David Schroeder From: gkg.the.lame@gmail.com [mailto:gkg.the.lame@gmail.com] On Behalf Of Kuba Krchak Sent: Thursday, January 7, 2016 1:35 AM To: David Schroeder; genealogy-dna@rootsweb.com Cc: Andreas West Subject: Re: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA David, this is no mystery, you yourself present the explanation. Ancestry has LESS SNPs along the pileup - 460 compared to 612 of 23andMe. This means you threshold of 5cM and !! 500 SNPs !! is too strict for pile-up only match of the A kit. It has to be supported by at least 40 cumulative SNP of IBS regions on both sides of the pileup. Whereas 23andMe can easily satisfy the 500 SNP threshold you set for your experiments. Setting the threshold to 400 SNPs should bring the number of pile-up matches for A kit up, while setting it to 700 SNPs should bring it down for the M kit to verify this theory. Best regards, Kuba On Wed, Jan 6, 2016 at 9:37 PM, David Schroeder via <genealogy-dna@rootsweb.com> wrote: For comparison for the matches I had on Chromosome = '15' and (POS > 23976155 AND POS < 25855576) My pileup region +-----------+---------+ | Fixed ANC | AVG(CM) | +-----------+---------+ | 119 | 10.2 | +-----------+---------+ +----------+---------+ | Orig ANC | AVG(CM) | +----------+---------+ | 150 | 10.0 | +----------+---------+ +---------------+---------+ | Fixed 23andme | AVG(CM) | +---------------+---------+ | 442 | 8.6 | +---------------+---------+ +--------------+---------+ | Orig 23andme | AVG(CM) | +--------------+---------+ | 556 | 8.3 | +--------------+---------+ It is a mystery to me why 23andme generated more matches in my pileup region. David Schroeder -----Original Message----- From: David Schroeder [mailto:dschroed991@sbcglobal.net] Sent: Wednesday, January 6, 2016 2:18 PM To: 'ahnen@awest.de'; 'genealogy-dna@rootsweb.com' Subject: RE: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA Sorry about the sea of information. There were so many comparisons, and each one had surprising results. I think I can say at least 25% of my matches coming from 23andme were from a Pile-up on Chromosome 15: POS > 23976155 and POS < 25855576). I looked at the two kits, Ancestry checks for 460 RSIDs in this range of positions. 23andme checks for 602. The pileups for Ancestry are much less than 23andme. Ancestry only had 12 no-calls in this region, 23andme only had 17. I don't know why there were hundreds more matches in this range for 23andme compared to Ancestry. David -----Original Message----- From: ahnen@awest.de [mailto:ahnen@awest.de] Sent: Wednesday, January 6, 2016 11:09 AM To: David Schroeder; genealogy-dna@rootsweb.com Subject: Re: [DNA] Raw Data Files Comparisons with 23andme and AncestryDNA David, A summary on the last comparisons would be fine. I've got lost in the many tables which despite your wonderful effort are still hard to read in plain email format. Great analysis! Andreas ------------------------------- To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com 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 GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message