Thanks Tim I'm really surprised at the number of SNPs in those IBS segments and equally surprised at the 10cM length. The SNP numbers in particular are way over the 700 I have seen stated to be long enough for a IBD match. I'm trying to think of reasons for such long IBS segments and here are my thoughts: 1. There is a very low allele variability in the population in those regions. However if that were so, then lots of people would be seeing those particular segments matching others and I don't think that is so? 2. The segments aren't really that long and Family Finder is tolerating too many mismatches. If that were so the the IBD segments would also be too long and I haven't heard anyone say that is so. I think it is important to understand why this is happening because if we could easily identify IBS segments then we could ignore them and save time and effort in trying to identify matches. Do you have any other ideas for the existence of long IBS segments? Duncan -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Tim Janzen Sent: 11 January 2012 08:05 To: [email protected] Subject: Re: [AUTOSOMAL-DNA] SUBJECT: How do you work a 5 way FF matchwith few clues Dear Duncan, I don't know how "smart" the matching algorism is for FF, but based on the results of my FF data, it seems to do a fairly good job of finding all or almost all of the appropriate matches assuming that the matching segment is over 9 cMs or so. You can find the allele frequencies for individual SNPs by going to http://www.ncbi.nlm.nih.gov/snp and entering the SNP of interest. If you have quite a few people on your 23andMe account then you can get a rough idea of the allele frequencies for individual SNPs by going to the "browse raw data" section, entering the SNP of interest and then reviewing the genotypes for the people on your account. The 3 matches for my wife and I that FF reported as being IBS that were between 10 and 11 cMs were on chromosome 20 (1900 SNPs), chromosome 7 (2400 SNPs), and chromosome 15 (2261 SNPs). Sincerely, Tim Janzen -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of r0berts0n Sent: Tuesday, January 10, 2012 2:35 AM To: [email protected] Subject: Re: [AUTOSOMAL-DNA] SUBJECT: How do you work a 5 way FF match with few clues Does anyone know how smart the matching algorithms are for Family Finder? My understanding is that each SNP in the 700,000+ has been selected because it has a useful allelle frequency in the general population. I don't know what the ranges are but presumably they run from 50/50 to 90/10 or beyond? If there are runs of consecutive SNPs that have a 90%/10% frequency in the European population, then a higher number of consecutive matching SNPs would be required to ensure an IBD match. Do the high numbers of IBS matches for 10-11cM occur in particular locations eg Chromosome 6? Duncan ______________________________ 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message ----- No virus found in this message. Checked by AVG - www.avg.com Version: 2012.0.1901 / Virus Database: 2109/4735 - Release Date: 01/10/12