Hi David, Oh, I was wondering what you were defining as a 'pile-up.' I did not appear to be having such a problem, and could think of several scenarios of what you could be referring to. I was thinking of your efinition of a 'pile-up' as in the HLA regions. (I identify those with a simple calculation that includes the number of SNPS....) Now I get it. I am now thinking that you are looking at your surname signature(?). Or, at worst, haplotype group signature(?). I get chromosomes with a high density of matching (tiny) segments on chromosomes 1 and 11 when using autosomal sampling from my Y-DNA surname project. I am thinking that I am looking at that as a basic signature for my surname, because of the criteria I use to match each segment triad. Those segments that I do not use in the triad include at least one HLA region on chromosome 6. That HLA region (in my small study) occurs in about 25% of my sampling (after processing). Hence the confusion for me in what you were using for the term 'pile-up.' Apparently, I would gather that a pile-up such as in an HLA region is not what you are referring to. I would think that you may be working on a method that might very well refine your targeted matching segments. I am curious if you have crossed checked the reductions against what surnames go missing? Alternatively, have you counted the number of the pile-up of surnames as well? (I am thinking that losing a random pool of names might be an indication of progress.) Or am I still not understanding the definition (as used here) for a pile-up region? - Dave Hamm RE: On 12/17/2015 2:59 AM, genealogy-dna-request@rootsweb.com wrote: > Date: Wed, 16 Dec 2015 14:41:33 -0600 > From: "David Schroeder"<dschroed991@sbcglobal.net> > Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs > AncestryDNA > To:<genealogy-dna@rootsweb.com> > Message-ID: <000001d13842$28cac770$7a605650$@net> > Content-Type: text/plain; charset="us-ascii" > > Continuing with my analysis of raw data files that have been 'fixed' for > no-calls using SNP information from matching RSIDs found in 23andme and > AncestryDNA. > > I uploaded the fixed files to gedmatch. My original kit from my 23andme was > already in place. I used the Tier 1 utility, "Matching Segment Search." I > used a minimum segment size of 5 cm without graphic. I downloaded the > matching list of segments into an Excel Spreadsheet. I used the segment > matches as I feel I get better information than the "one-to-many." > > Here are my results: > > 1925 gedmatch_segment_matches_M080859 (original 23andme kit with a 2.2 % > error rate) > > 1741 gedmatch_segment_matches_M306764 (fixed 23andme kit with a 1.5 % error > rate- about a 10% reduction in segment matches) > > 1263 gedmatch_segment_matches_A146269 (fixed Ancestry kit with a 1.0% error > rate - I haven't uploaded my original AncestryDNA file) > > I do have issues with a lot of pileups on chromosome 15: > > Number of Segment Matches on Chromosome 15 - large number of pileups > Original 23andme: 603 > Fixed 23andme: 482 > Fixed Ancestry: 197 > > Compared to number of Segment Matches on Chromosome 6: > Original 23andme: 75 > Fixed 23andme: 82 > Fixed Ancestry: 84 > > It is an interesting situation. I expected fewer matches on my fixed kit, > but I did not expect so much less on my ancestry kit. Any ideas why? I am > going to dig deeper into the data. > > David --