GedMatch’s Full Matching Base Pairs

Kitty Cooper had a blog entry – “When is a DNA segment match a real match? IBD or IBS or IBC?” that discussed a problem when it comes to matches, some of these are not true matches due to the fact that when we share a matching segment with someone of a common ancestor, it is based on half identical regions.  We basically get a set of alleles from each parent but genome testing looks for stretches of DNA, however it cannot figure out whether it came from your father or mother.  This is what can cause problems with matches because they may not be a true match.  More about this can be found here:

When doing a ONE TO ONE comparison on, you have the option to show a graphical bar for each chromosome that is color coded and it can show where on a chromosome you match half of the base pairs, or have a full match.  Usually the full matches are seen when being compared to siblings.  Parts of it will be green, the other yellow, and also red.  When compared to an identical twin, it will be all green.

Screen Shot 2014-11-06 at 5.51.43 PM

This is what it looks like when comparing my kit to my half-brother’s.  Below are only a few of the chromosomes where we match, but you can see where the blue is under the yellow.  Blue indicates that the segments are at least 7cM and the yellow indicates that it is a half match base pair.

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Since Polynesian are super endogamous, resulting from successive founding populations and bottle necking events, it is not unusual to see full matching base pairs in green.  Below is what it looks like when comparing my mother to my friend’s father.


I am only showing four of the chromosomes, the chromsomes that had the most full base pair matches.

We are not close relatives, but my mother does share a lot with him.  These are the segments shared between my friend’s father and my mother.  Only chromosomes 1 and 3 show no green segments.  All the others do have green segments.


What this means is that both pairs of each chromosomes are matching.  So my mother’s parents and my friend’s paternal grandparents were all related.  When doing a ONE TO ONE comparison, it is usually easier to compare without the graphs, unless you are looking for something specific, like with identical twins or full versus half-siblings. In the case of endogamy however, it may or may not be useful, depending on what you are looking for.  If you are simply looking for a match, then it is not needed.  I wrote in a previous blog entry about multiple small segments as a key for endogamy, using a graph may give a better insight with how much you may be related to someone, or rather how many times you may descend from common ancestors.

Although I have not made an in-depth comparison yet, but from what I can tell it seems that the majority of the green bars indicating a full base pair match is more noticeable when comparing my mother with other Hawaiians.  I compared all the known Maori matches who share more totals with my mother versus Hawaiians who do not share as much, and from what I can see is that they do show a few tiny green segments.  The most obvious is that the less admixed the Polynesian,  the easier it is to see more green segments.  This makes logical sense and of course the amount of green would be more indicative of ties to a specific geographic area, or rather indicate that people have remained in a specific geographic area for a longer amount of time.  This too should be obvious by the multiple number of segments.

So to summarize, the full base pairs (green) means that there are multiple lines of relationship, more specifically to the parents of the matches if the amount of green segments are large or nearly matches the blue bar indicating matching segments great than 7cM.  While the multiple segments would indicate descending from a common ancestor multiple times.


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