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
