Karen, I think maybe Tim answered your question, but just to be sure, FF is always reporting one side of the double helix (called the plus side). The two bases you see in the raw data are from the two copies of the chromosomes, the maternal and the paternal (each one is a separate double helix). The two-base combo is called a genotype, and the two bases are called alleles. We don't know which allele came from the father and which from the mother, though, so the alleles are always given in a standard order. At 23andMe this is alphabetical. At FTDNA, it's not always alphabetical, but you see only these combinations (plus special codes for no-calls, insertions, and deletions) AC AG AT CG TC TG For a half-identical region (HIR), at least one of the two alleles in the first person must match at least one of the two alleles in the second person. We look for long consecutive runs where this occurs. In Tim's example, you would almost never see the combinations in SNPs #6 and 7, with three different possible alleles. Almost all SNPs are bi-allelic, since the mutation rate is so low. Practically speaking, the only way a run terminates is with opposite homozygotes (each person's own two alleles are the same, but the two people differ from each other, e.g. AA in one person and GG in the other person). Ann Turner On Sat, Jan 7, 2012 at 9:58 PM, Tim Janzen <[email protected]> wrote: > Dear Karen, > No the program "doesn't keep to one side". Let's consider some imaginary > data as follows for two people's comparison: > > #1 #2 > AA AG > GG GT > TT TG > AG GG > AC CC > TA AC > GG TC > > Note that in the above example the program would indicate that the alleles > for first 6 SNPs would be part of a half identical region (HIR) but the > program would stop the HIR at the 7th SNP. Keep in mind that the raw data > coming out of the SNP chip test is not phased. In other words, you can't > tell which chromosome the allele is from simply by looking at the results. > This is the reason why it is nice to phase the SNP chip data. However, the > results from Family Finder and 23andMe are in the plus (or forward) strand > orientation. See http://www.ks.uiuc.edu/Research/hemolysin/3versus5 and > http://www.imgt.org/IMGTindex/dnaStrand.html for background on the strand > orientation issue. > Sincerely, > Tim > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Karen Hodges > Sent: Saturday, January 07, 2012 9:28 PM > To: [email protected] > Subject: Re: [AUTOSOMAL-DNA] segment matches > > Hi Tim > > Thanks but does it keep to one side when matching[ all from the right side > of the dna backbone or all from the left side of the dna backbone] or are > some matches a mix, jumping between sides[taking some readings from the > left and right of the dna segment] ? > > Karen > > > > > ______________________________ > 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 >