[Genome] rsids mapping to multiple locations

[Ewan Birney]

On 22 Apr 2007, at 22:19, Amit Indap wrote:

>
> Hi UCSC
>
> Sorry if I should be directing this to the  folks at
> dbSNP, but I found a couple hundred rsids that map to
> 2 locations: a real chromosome and then to a
> chrom*_random.
>
> I was surprised to come across this. My guess these
> records are passing their quality checks on snp
> mapping at dbSNP. Some examples:
>
> rs17139617 at chrX_random:1079290-1079790
> rs17139617 at chrX:77161265-77161765
>
> rs17732842 at chr3_random:293033-293533
> rs17732842 at chr3:76384194-76384694
>
>

this is entirely expected, in particular for the xxx_random cases,
which are regions that are suspected to be involved in the human
genome reference, but currently unplaced, usually because of
segmental duplication. There will be other cases where an rsid
will map to > 1 place on the reference chromosomes as well.

It is the investigator's choice about what to do with this information.
Keep the location on the reference, discard the other? discard both?
process with both on.


This is more biology and less a data mapping bug (though bugs do
sometimes come out with this 2-mapping phenotype, most things
mapping > 1 location is an issue about SNPs defined in segmental
duplications and/or low-copy repeats).




> Amit Indap
> Cornell University
>
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