Thank you everyone for your insight! I ran some more comparisons of my raw data files AncestryDNA vs 23andme: 1). I had only 4 RSIDs that began with an 'i' that had a real RS number on my AncestryDNA file. 2). I had 108 RSIDs that appear to not match on the SNP pairs between Ancestry and 23andme. Perhaps they could be labeled mis-calls? 3). I had a total of 7646 no-calls on autosomal chromosomes for RSIDs that appear both on AncestryDNA and 23andme 4). I had a total of 11,779 no-calls on 23andme autosomal chromosomes. I had 21,893 if you include the X, Y, and Mt. 5). I had a total of 7,798 no calls on Ancestry DNA autosomal chromosomes. I should be able to fix my no-calls for both 23andme and AncestryDNA. David **************************************************************************** * Dear David, DD means a deletion and II means an insertion. The "i" SNPs in the 23andMe files are those that don't have rs numbers assigned to them by 23andMe. It is possible that "i" stands for Illumina, but I am not certain about that. It is also possible that it stands for "inserted", possibly because 23andMe inserted these SNPs onto the SNP chip because they were of special interest to 23andMe. Someone at 23andMe would know the answer to this question. It is interesting that AncestryDNA files don't have SNPs with the allele values AT. I don't have a definite answer for that. I checked my mom's file for the SNPs that have the allele values AT in 23andMe and found a total of 322 of these SNPs. I then checked for these SNPs in my mom's AncestryDNA file and I couldn't find any of those SNPs in my mom's AncestryDNA file. My suspicion is that Ancestry.com has dropped all SNPs from their dataset with the values AT because they think that the results may be erroneous. Sincerely, Tim Janzen -----Original Message----- From: genealogy-dna-bounces@rootsweb.com [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of David Schroeder via Sent: Saturday, December 12, 2015 9:33 PM To: genealogy-dna@rootsweb.com Subject: [DNA] My Raw Data Files - Comparison 23andme vs AncestryDNA I have tested at both 23andme (V3) and AncestryDNA. I have written a program to add the raw data file information into a MySQL database, creating separate tables for my 23andme results and my AncestryDNA. I am trying to understand some things. I can understand all the A, C, G, T lettering. The single letters represent SNPs on my Y and X chromosomes. I also understand that '--' is a no call. What are 'DD' and 'II'? I also found that AncestryDNA had no 'AT' SNPs for me, but 23andme had 611: Can anyone explain why I have no 'AT' SNP pairs in my AncestryDNA raw data file? I verified this by browsing my Ancestry Raw data file. I had every other SNP pair represented. The final question is about RSIDs. What are the ones that begin with 'i' in my 23andme raw data file? I have 10,709 RSIDs that begin with 'i-----'. David