Dear Mary, Thank you so much for your response! I searched rs100 in UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg19&position=rs100&hgt.suggest=&pix=800&Submit=submit). In snp130, it was mapped to chr7:24438349 only. But in snp131, it was mapped to other 6 locations. I think that UCSC mapped snp130 to GRCh37/hg19, which is consistent with SNP mapping of Ensembl. I will send an email to ask the dbSNP team.
Thanks, Hong -----Original Message----- From: Mary Goldman [mailto:[email protected]] Sent: Monday, June 21, 2010 9:25 PM To: Xu, Hong (NIH/NIEHS) [E] Cc: [email protected] Subject: Re: [Genome] something is wrong in snp131.txt file? Hi Hong, We obtain all of our mappings from dbSNP; you can find more information about how they align SNPs at http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq&part=Build.The_dbSNP_Mapping_Process. Please note their results may differ from what is obtained from BLAT since they use BLAST and MegaBLAST. Additionally, if you BLAT the flanking sequences of rs100 you will notice that while there is one top hit, there are many other hits that align almost perfectly (90-100% identity), so it is not surprising that dbSNP has mapped it to multiple locations. Feel free to contact dbSNP at snp-admin at ncbi.nlm.nih.gov if you have any questions about their web pages (in particular, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=100 and the wording therein) or how SNPs are mapped. 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 6/21/10 12:49 PM, Xu, Hong (NIH/NIEHS) [E] wrote: > Dear UCSC developer, > > I just downloaded the newly released snp131.txt file from UCSC FTP server. I > found something wrong with at least one SNP mapping - rs100: > $ grep "rs100 " snp131.txt > 989 chr15 53033239 53033240 rs100 0 + G > G A/G genomic single by-cluster 0.5 0 unknown > exact 3 > 785 chr18 26276338 26276339 rs100 0 - T > T A/G genomic single by-cluster 0.5 0 unknown > exact 3 > 2023 chr2 188538478 188538479 rs100 0 - C > C A/G genomic single by-cluster 0.5 0 unknown > exact 3 > 882 chr21 38962576 38962577 rs100 0 - T > T A/G genomic single by-cluster 0.5 0 unknown > exact 3 > 1632 chr3 137316782 137316783 rs100 0 + G > G A/G genomic single by-cluster 0.5 0 unknown > exact 3 > 1661 chr4 141137111 141137112 rs100 0 + G > G A/G genomic single by-cluster 0.5 0 unknown > exact 3 > > rs100<http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp&cmd=search&term=rs100> > were mapped to 6 human genome locations. None of them was correct. The > correct one should be chr7: 24438349 if you BLAT rs100 sequence to the latest > human genome (GRCh37). I checked dbSNP. It states that > "rs100<http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=100> [Homo > sapiens]Mapped unambiguously on non-reference assembly only". How could this > problem happen? > > Thanks a lot, > Hong > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
