[Genome] SNP

Davidson, S. s.davidson at abdn.ac.uk
Mon Jul 2 05:43:58 PDT 2007


Hi UCSC,
I wonder if you can clear something up for me.
I'm looking at Human Mar. 2006 Assembly and I'm interested in the SNP
track.
 
I was looking at the source data used to create this track, in
particular the b126_SNPContigLoc_36_1.bcp.gz file from dbSNP.
I noticed that the coordinates given for the SNPs don't match the
coordinates displayed on the browser.
For example (the first SNPs in the file):
 
snp    dbsnp_coordinate    UCSC_coordinate
rs3        31344841                    31344842
rs4        31345221                    31345222
 
However when I looked within UCSC text files from the table browser I
saw that these SNPs are noted as having a chromstart and chromend
positions
 
        chromstart    chromend
rs3    31344841    31344842
rs4    31345221    31345222
 
This suggests that dbSNP uses a different coordinate convention to the
zero based start one based end that UCSC employs, am I right in thinking
this?
 
Thanks in advance,
Scott



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