Hello: I would like to use the allele frequency data in snp132Common (hg19). But I don't understand some of the "alleles" in column 23 of this table.
For example, here is the table row for rs2229621: 1157 chr2 75099476 75099477 rs2229621 0 + A A A/T genomic single by-cluster,by-frequency,by-submitter,by-hapmap,by-1000genomes 0.378067 0.214706 missense exact 1 15 1000GENOMES,APPLERA_GI,BGI,CANCER-GENOME,COMPLETE_GENOMICS,CSHL-HAPMAP,EGP_SNPS,HGSV,IBARROSO,ILLUMINA,IMCJ-GDT,PERLEGEN,SEATTLESEQ,WICVAR,YUSUKE, 3 T,A,0, 423.000000,299.000000,6.000000, 0.581044,0.410714,0.008242, maf-5-some-pop,maf-5-all-pops Column 23 is: T,A,0, What does "0" mean? (These "0"s are very common for chrX.) Another example, here is rs3215906: 764 chr1 23518470 23518471 rs3215906 0 - A A -/T genomic deletion by-cluster,by-frequency 0.270941 0.249121 unknown exact1 4 BUSHMAN,DEVINE_LAB,SNP500CANCER,YUSUKE, 3 T,-,+, 1.000000,62.000000,331.000000, 0.002538,0.157360,0.840102, maf-5-some-pop,maf-5-all-pops Column 23 is: T,-,+, What does "+" mean? Have a nice day, Martin Frith http://www.cbrc.jp/~martin/ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
