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
