Hi Huang-Wen, That is our representation for insertions into the reference genome. The length of the item is 0 in the reference genome, and greater than 0 for the insertion alleles.
In our internal 0-based, half-open coordinate system, start is equal to end when length is 0 (chr1 10433 10433). To convert our internal coordinates to the 1-based, fully-closed coords that everyone expects, we add 1 to the start position, so that becomes the chr1:10434-10433 that you see in the browser. It looks odd, but the usual 1-based length calculation (end - start + 1) works out to 0. For more information on our 0-based, half-open coordinate system, please see this FAQ: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Huang-Wen Chen wrote, On 3/18/2011 10:54 AM: > Hi, > > snp131 contains ~10% of records with a property that the start position > is greater than the end position. For example, we saw > "Position: chr1:10434-10433" for rs56289060. The regions they described > are correct according to dbSNP, except that the start and end position > are reversed (this happens even on the sense strand). Is there any > special reason for this reverse representation of regions ? Or, any plan > to swap them such that chromStart< chromEnd holds for consistency ? > Thanks .. > > ---- > Huang-Wen (Howard) Chen, Ph.D. > Email: [email protected] > Phone: (215) 503-6151 > > Computational Medicine Center > Jefferson Medical College > Thomas Jefferson University > http://cm.jefferson.edu > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
