Hi Jiangtao, The engineer who works on SNPs here took a quick look at your examples. For the first one, there may have been a strand error that caused dbSNP to fail to cluster the newer SNP (rs61770168) together with the older SNP (rs3115865). For the second example, you may just want to ignore rs28658281, since it aligns to multiple places in the genome and has been given a higher weight by dbSNP.
In both cases, you should check out dbSNP's pages (which are linked on the details pages in the Genome Browser). For instance: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3115865 There you can see the full report on each reference SNP (which start with an "rs" -- we only show reference SNPs in the Genome Browser), and you can look at the list of submitter SNPs (which start with "ss") that were used to determine each reference SNP. You might also want to report these cases directly to dbSNP at [email protected]. I hope this is helpful. If you have further questions for UCSC, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 05/26/11 21:58, Tao Jiang wrote: > Dear UCSC bioinformatic scientists: > > When use the file "snp132.txt.gz" downloaded from UCSC, I found a confusion > question: Why the SNPs that have exactly the same start and end coordinates > have different rsID, and sometimes have different allele frequency? Which > record is the refSNP record from NCBI dbSNP 132? > > The following are two examples: > 1. > 590 chr1 741578 741579 rs3115865 0 - T T > A/G genomic single by-cluster,by-hapmap 0 0 unknown > exact 3 > 590 chr1 741578 741579 rs61770168 0 + T T > C/T genomic single unknown 0 0 unknown exact 1 > 1 > > 2. > 707 chr22 16050993 16050994 rs7288968 0 + > G G C/G genomic single by-cluster,by-2hit-2allele,by-hapmap > 0 0 unknown exact 1 2 > BCM_SSAHASNP,CSHL-HAPMAP, 0 > 707 chr22 16050993 16050994 rs28658281 0 - > G G C/G genomic single by-cluster,by-frequency 0.375 > 0.216506 unknownexact 3 MultipleAlignments 6 > BCM-HGSC-SUB,BCMHGSC_JDW,BGI,ENSEMBL,HGSV,SSAHASNP, 2 G,C, > 6.000000,2.000000, 0.750000,0.250000, maf-5-some-pop,maf-5-all-pops > > > I am looking forward to hearing from you as soon as possible. Thanks a lot! > > All my best, > > Jiangtao > > BGI-Shenzhen > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
