Hi Ying, The genomic locations for SNPs come directly from dbSNP. dbSNP aligns submitted flanking sequences to the genome, and clusters the aligned coordinates to make the reference SNPs (rs#). Sometimes the flanking sequences map to multiple places in the genome, especially when they fall in highly similar regions such as segmental duplications or paralogs. When a SNP aligns to multiple loci, dbSNP assigns it a weight > 1 (see the last column in rows from snp128 - snp131). In cases like this, one may question whether there is true polymorphism, or just similar but not identical sequences in the genome.
The track "Segmental Dups", also in the Variation and Repeats group of tracks, shows that both mappings of rs648663 fall within annotated duplications of chr22 regions (and chr1). If you click on rs648663 in the Genome Browser, and then click on the "+" button for the "Re-alignment of the SNP's flanking sequences to the genomic sequence" section, you can copy the flanking sequence for rs648663: ATTATTTAATTATCAAATTTGTGTGTCTGATGATCCTTTACAACACTGCAGCATCAAATAAAGTGTTATCAGATTtctttcttttttttttttttgagac tgggtctgattctgtagcccaggctggagtgcaggggtataataatagctcactgcagcttcaaactcctgagtttgtttgtttgtttgtctgtttgtct gtttgtttgtttggagagacagcgtctcgaactcctgggctccagtgatcctcccacctcagcctcccaaagtgctgggattacaagcatgagccactgt gcccCAGCCCAACATCTGATTTCAAAAGTACTATTGATATTATAATCACCATTAAAAATCACTGAAGTTTTTGTCACCCAAAGTTTTACTTTGAAATATA GAACATTTCATTTTTTTCCCACACACCTCACATCTGCTTTTGATTTTTAACATGTGCATGAATTACCTCTTATTAGAAAAAAAA M CACAAAATTTTTTGGTAAAAGAATTATCTTAAGTGGGTATTTTTTCCCTAAGTCTGAAATGACTTAGTAAGGATAAGAGGTCAAACCATATGCTTTGTAG TGAAACTGCAACTATGATGAATAACATTAGAATTCTGGATGCCTTCCAGCAGCTGGAACAGGGCAGACCTGAGGCGGGAGTCCTCATGCTTAGGGGAAGG GGCTCAGGCACTGGGAGTCGGTCAGGGCTCCCAGGATGTAAAAGATACACATGAAAGAAACAAACAGTGGGACTCGGGCCAGTGCAAAATTTGGCCTGGA ACTGAGCTAAAAACTGTCATACTGGTGGGAAGAAGCAGATTGGTTCAACAGGGTAACCAAATGTGAAAAAGAAAAGCCTCACAAGAATTAAAATTGATGG TTGGAACTGGGCGCTCCGAGGCTGTGGGCCGGTGTCCTGCCCCGAAGGGTTTGGCTGCCAGCAGGTGCAGCGCTGCCCTGGGATACCAGC -- then click on the "Blat" link in the blue bar at the top of the page, paste the sequence there and click submit. There is a perfect match to the chr22 17M location, and a close but not perfect match to chr22 19M. There is also a 96% identity match to chr1 116M. (These locations are in NCBI36/hg18 coords for snp128, snp129; coords in GRCh37/hg19 for snp130-snp132 are ~1.6M larger due to assembly updates.) To dig even further, you could click through to dbSNP's report page for rs648663 from our details page, and compare the different submissions' flanking sequences... are they identical, or does one more closely match the chr22 19M genomic sequence? Or you might consider excluding SNPs from analysis if they have been mapped to multiple genomic loci (weight column > 1; in snp132, flagged with MultipleAlignments in exceptions column). Hope that helps, Angie ----- "Ying Sun [BSD] - HGD" <[email protected]> wrote: > From: "Ying Sun [BSD] - HGD" <[email protected]> > To: "Mary Goldman" <[email protected]> > Cc: [email protected] > Sent: Wednesday, June 8, 2011 8:55:19 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Question for multi locus for single SNP > > Hi Mary, > > I have another question need your help. I have 5 version snp > downloaded. However, I found that some SNPs have quite different > locus even in the same file (for example the one rs648663 I attached > below). And it looks like all the other information is the same. > Would you please let me know why it's in such way? Thanks a lot. > > Ying > > > =============================== > snp128_chr22:716 chr22 17187821 17187822 > rs648663 0 + A A A/C genomic single > by-2hit-2allele 0 0 intron > exact 1 > > snp129_chr22:716 chr22 17187821 17187822 > rs648663 0 + A A A/C genomic single > by-2hit-2allele 0 0 intron > exact 2 > snp129_chr22:737 chr22 19939068 19939069 > rs648663 0 + A A A/C genomic single > by-2hit-2allele 0 0 intron > exact 2 > > snp130_chr22:728 chr22 18807821 18807822 > rs648663 0 + A A A/C genomic single > by-2hit-2allele 0 0 unknow > n exact 2 > snp130_chr22:749 chr22 21609068 21609069 > rs648663 0 + A A A/C genomic single > by-2hit-2allele 0 0 unknow > n exact 2 > > snp131_chr22:728 chr22 18807821 18807822 > rs648663 0 + A A A/C genomic single > by-cluster,by-2hit-2allele 0 0intron exact 2 > snp131_chr22:749 chr22 21609068 21609069 > rs648663 0 + A A A/C genomic single > by-cluster,by-2hit-2allele 0 - > 0 intron exact 2 > > snp132_chr22:728 chr22 18807821 18807822 > rs648663 0 + A A A/C genomic single > by-cluster,by-2hit-2allele 0 0intron exact 2 > MultipleAlignments 7 > BCM-HGSC-SUB,BCMHGSC_JDW,GMI,SC_JCM,SC_SNP,SSAHASNP,TSC-CSHL, 0 > snp132_chr22:749 chr22 21609068 21609069 > rs648663 0 + A A A/C genomic single > by-cluster,by-2hit-2allele 0 0intron exact 2 > MultipleAlignments 7 > BCM-HGSC-SUB,BCMHGSC_JDW,GMI,SC_JCM,SC_SNP,SSAHASNP,TSC-CSHL, 0 > > > ________________________________ > > From: Sun, Ying [BSD] - HGD > Sent: Wed 6/8/2011 9:33 AM > To: Mary Goldman > Cc: [email protected] > Subject: RE: [Genome] snp132 chr14 download problem > > > It works perfectly now. Thanks. > > Best, > Ying > > ________________________________ > > From: Mary Goldman [mailto:[email protected]] > Sent: Tue 6/7/2011 5:25 PM > To: Sun, Ying [BSD] - HGD > Cc: [email protected] > Subject: Re: [Genome] snp132 chr14 download problem > > > > Hi Ying, > > I'm sorry, but I was not able to reproduce your error. Is it possible > that the file was somehow corrupted during the download? Have you > tried > to re-download the file? > > If you are downloading an entire table, especially a large table such > as > snp132, we highly recommend using our downloads server. Once you > download the file, you can separate the snp records into different > files > based on chromosome. > > To get to our downloads server, start at our homepage > (http://genome.ucsc.edu/) and click on "Downloads" in our blue side > bar. > >From there, click on "Human" and scroll down to the section on hg19. > Click on the "Annotation Database" link and then click on > "snp132.txt.gz" link to download that file. The resulting link should > be: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz. > > I hope this information is helpful. Please feel free to contact the > mail list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 6/7/11 2:32 PM, Sun, Ying [BSD] - HGD wrote: > > To whom it may concern, > > > > I am downloading dbsnp132 for all chromosomes at > http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=197503545&clade=mammal&org=Human&db=hg19&hgta_group=varRep&hgta_track=snp132&hgta_table=0&hgta_regionType=range&position=chr14&hgta_outputType=primaryTable&hgta_outFileName=snp132_chr14, > and everything works fine except chromosome 14. When I tried to > gunzip it on Linux server, it always get error message "gunzip: > snp132_chr14.gz: unexpected end of file". Please help to figure it > out. Thanks a lot. > > > > Sincerely, > > Ying Sun > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > This email is intended only for the use of the individual or entity to > which it is addressed and may contain information that is privileged > and confidential. If the reader of this email message is not the > intended recipient, you are hereby notified that any dissemination, > distribution, or copying of this communication is prohibited. If you > have received this email in error, please notify the sender and > destroy/delete all copies of the transmittal. Thank you. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
