Measuring Segments

For autosomal DNA, segments are measured 3 ways:

base pairs (bp) – these are the individual building blocks (molecules) that form each chromosome. Over the entire set of chromosomes there are 3.2 billion base pairs. Each chromosome has from 48 to 250 million base pairs. So a segment can be defined by the Start Location and End Location. Think of base pairs as a physical picture of a segment – it’s physical length and location on a chromosome.

Example: Start at 23,500,000; End at 46,300,000

Many of us round to the closest Megabasepair (Mbp). A Mbp is 1,000,000 bp

Example: The segment is 23.5-46.3Mbp

Rounding makes these numbers much easier to read and to type. And, in my opinion, there is virtually nothing lost in accuracy. Mbp is just fine for genealogy, triangulation and chromosome mapping. If you want to do some analysis of a particular part of a segment for some scientific or medical reason, you may want to use bp. (I’ll discuss “fuzzy data” and “fuzzy segments” in a separate blog post)

centiMorgans (cM) – I think of cM as a “quality” factor, or a “genetic distance” of sorts. The cM is the best measure we have of genetic distance, but it is far from perfect. The cM is empirically derived – that is scientists have recorded many observations and put them into tables. From these tables the cM value between any two points on a chromosome (as measured by bp) can be determined. In very general terms, more is better, and the larger the cM of a shared segment, the closer the Match would be. DNA is very random, and there are wide ranges of cM vs cousinship (including much overlap).  See these references for more info [1], [2] and [3].

Example: A segment may be 15.4cM

SNPs – the single molecules (nucleotides), or base pairs, which show some amount of variation in human DNA. Most (99%) of our DNA is the same. For genealogy, we are looking for SNPs (sometimes referred to as markers) which are known to vary. The difference in our SNPs is what sets us apart. Basically each SNP can have one of 4 values: A, C, G or T. Each of the autosomal DNA testing companies uses a slightly different “chip” to determine these values, and they each effectively test a different number of SNPs – usually in the range of 600,000 to 700,000 SNPs. These are spread out over all of your chromosomes – think of them as a sampling of your DNA (a sampling of the most variable parts of your DNA). This might range from about 10,000 SNPs on the smallest chromosomes to over 58,000 on Chromosome 1.

Example: A segment may include 2,451 SNPs

Note that there is no firm correlation between these measurements. We can convert temperature measured in Centigrade to Fahrenheit because they both measure the same thing. All of the above measurements, measure different things. However, on average, there are about 100 cM for 100 Mbp

So, in summary:

A segment may be described: Chr 6: 23,500,000 to 46,300,000; 15.4cM; 2451 SNPs

A short cut description may be 6: 23.5-46.3Mbp; 15.4cM; 2451 SNPs

References:

[1] http://www.isogg.org/wiki/CentiMorgan

[2] http://en.wikipedia.org/wiki/Centimorgan

[3] http://compgen4.rutgers.edu/mapinterpolator

03 Segmentology: Measuring Segments; by Jim Bartlett 20150513

17 thoughts on “Measuring Segments

  1. Thanks, Jim. I was informed of your blog via Roberta’s. This “Segmentology” series are excellent! I’m able to apply immediate the methodology you’ve outlined. I’m also currently in a family project in which triangulation is proving to be an exceptionally helpful tool in deconstructing and reconstruction the “yellow brick road” to our common ancestor.

    Liked by 1 person

  2. Hi Jim,
    I’m struggling a bit with the SNPS, so based on your comment, if I have results like below, that does not tell me anything other than the 16cm match is closer (in terms of generations) than the others? Here are a few examples,

    Match A with 16 cm 700 SNPS
    Match B with 9 cm 2800 SNPS
    Match C with 9 cm 500 SNPS

    If SNPS aren’t useful, to determine something, I’m wondering why this info is included Does it matter if the matches above were on the same chromosome (other than Match A is a closer cousin)? Told you I was confused!

    Thank

    Like

  3. The SNPS may sometimes be a secondary measure, but not often. The 16cM segment is always good. The 9cM segment with the fewest SNPs is suspicious. I’d make sure that one matched at least 3 others.

    Like

  4. Hello Jim,
    I am a newbie to all of this but I found your article very interesting and understandable to someone with limited knowledge of DNA.
    I tested at Ancestry and 23andme, then uploaded to Family Tree DNA and Gedmatch. Last night I was reviewing some information.
    I was just reviewing mt DNA results on Family Tree DNA. I noticed that 21 of my matches matched me on Chromosone 19 at the exact range and they all had 8.15 cM. I also noticed that another seven matches were 9.14 cM at another spot on Chromosone 19, I have many more matches to compare but stopped when I noticed this pattern emerging. Is any of the information relevant? Does it means anything. My father is unknown to me. Thank you in advance for your help. Cheryl Glenn Bradley

    Like

      • Hello Jim, I am not sure what you mean about a pileup. I have checked the matches with me in the chromosone browser on FTDNA and we all match. I am not sure what to do next. Thank you for answering me.
        I do have a higher person on FTDNA who has a total of 127.61 and the longest is 60.22 on Chromosone 11 and 49.99 on Chromosone 17. There are two other matches who are on Chromosone 10 and one is 28.14 and the other is 30.73. From what I read and if I understand it, I might be able to find a common ancestor with them as their matches are higher in number. Is that correct? Since I do not know who my father is and have no information on him, is it possible to determine how I am related to these matches and how? Thank you so much for answering me.
        With Warmest Regards, Cheryl

        Like

  5. Cheryl

    You say you used the Chromosome Browser and found all of these segments “matched”. Yes, you can use the CB and determine they all match you at the same location; but no, this does not mean that they match each other. At FTDNA it is impossible to check two of your matches to see if they match each other. You have to check them using In Common With to see if they are ICW each other.

    Like

  6. Jim, what do you make of a match that shows a single large segment match but not much else. Several times I have found a match of over 20 cM on one chromosome but nothing else over the default (7cM) threshold level anywhere else.

    Like

  7. Pingback: Fuzzy Data, Fuzzy Segments – No Worry | segment-ology

  8. Pingback: The Porcupine Chart | segment-ology

  9. Pingback: Getting Started with GEDmatch | segment-ology

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s