Q: What is YFull's "SNP matches" methodology?
A: The methodology is reflected in the SNP matches table, which provides information about Shared SNPs and Assumed Shared SNPs of compared samples. The table is limited to SNPs having an estimated age of 3500 ybp or younger (using TMRCA from the YTree), with a maximum of 100 lines of information.
Match information is given for the sample selected (selection box in the upper left hand corner of the table) and for each of the samples listed in the rows of the table.
The column headings of the table:
MRCA branch: MRCA means "Most Recent Common Ancestor."
TMRCA CI xx% ybp: Time to Most Recent Common Ancestor and Confidence Interval information from the YTree for the MRCA branch.
Most distant ancestor and country of origin: Information provided by the sample owner or manager (but not always provided). YFull does not try to verify that this information is accurate.
YFull ID and PM: YFull ID is the YFull identification number for a sample, and PM is a link to YFull's private message system, allowing the owner or manager of a YFxxxxx sample to contact the owner or manager of another YFxxxxx sample (but not scientific samples such as HGxxxxx, NAxxxxx and ERSxxxxxx).
Terminal Hg: The Haplogroup or branch with the youngest estimated age (age closest to the present) for a sample in the YFull database. In the context of the YTree, which is frequently updated to include new samples and new branches, Terminal Hg means the most recent branch discovered for a sample as of the time of a specific YTree revision.
Shared SNPs: When YFull compares a SNP in the raw data file of the selected sample with the same SNP in the raw data file of a sample listed in the table, and both samples are positive, then the compared SNP is placed in the "Shared SNP" category. The names of all Shared SNPs for compared samples are given in the pop-up window (select the magnifying glass icon) for the sample listed in the table.
Assumed Shared SNPs: When YFull compares a SNP in the raw data file of the selected sample with the same SNP in the raw data file of a compared sample, and one of the following three situations is present, then the compared SNP is placed in the "Assumed Shared SNP" category:
|Selected sample uncertain||Compared sample positive|
|Selected sample positive||Compared sample uncertain|
|Selected sample uncertain||Compared sample uncertain|
The names of all Assumed Shared SNPs for compared samples are given in the pop-up window (select the magnifying glass icon) for the sample listed in the table. "Sample uncertain" includes "no call."
The following five situations do not result in an Assumed Shared SNP:
|Selected sample positive||Compared sample negative|
|Selected sample uncertain||Compared sample negative|
|Selected sample negative||Compared sample positive|
|Selected sample negative||Compared sample uncertain|
|Selected sample negative||Compared sample negative|
"Sample uncertain" includes "no call."
All Shared SNPs: The total of Shared SNPs and Assumed Shared SNPs.
Last updated on March 28, 2018.