1

The second column of Ancestry's DNA results download is the chromosome number:

rsid    chromosome  position    allele1 allele2
rs3131972   1   752721  G   G

But it goes from one to 26! What's up with that?

WGroleau@MBP ~ % for PART in head tail; do
for> awk '{print $2}' /Users/WGroleau/DNA/AncestryDNA-WWG.txt  | sort -un | $PART -2
for> done
raw
1
25
26

1 Answer 1

4

Someone pointed me to https://www.snpedia.com/index.php/Ancestry.com which says:

  • If the Ancestry.com data file says a SNP is from chromosome 23, it's actually from the X chromosome.
  • If it indicates chromosome 24, it's from the portion of the Y chromosome that is not part of the pseudoautosomal region.
  • If it indicates chromosome 25, the designated SNP is from the pseudoautosomal region of the Y chromosome.
  • If it indicates chromosome 26, it's mitochondrial data (which is present in at least some Ancestry data produced since May 2016).
2
  • I dont think that is correct, because Chromosome 24 to 26 also have two allels listet and that means one is from mother and one from the father, so it is weird if it would only be x or y
    – Saskia
    May 1 at 1:00
  • The way the chip works is it finds all the alleles at a specific position on a specific chromosome. If they are nearly all the same, it will give two readings of the value. If there a significant number of differences, then it will give one reading of each value. This is done for all chromosomes. Ancestry doesn't clean the results, but gives you what it determines, even on X, Y and mt. You will find that on Y and mt and X for males, that the 2 values Ancestry gives are almost always the same, and the few that are not are because of read errors.
    – lkessler
    May 1 at 1:29

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