Hi all, ??? We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on? SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency. What statistical test should I use? My table looks like Chromosome ? ? ? ? ? position ? ? ? ? ? ? ? Major/minor Resequencing ? ? ? ? ? ? ? ? SNP array chromosome 1 ? ? ? ? 198432 ? ? ? ? ? ? ? ? C/T ? 75/13????????????????????????? 1460/280 chromosome 1 ? ? ? ? 14282752 ? ? ? ? ? ? A/G 69/19 ??????????????????????????? 1380/360 chromosome 1 ? ? ? ?? 595434 ? ? ? ? ? ? ?? T/G ? 83/5 ????????????????????????????? 1680/60 I really appreciate any guidance. Thanks Scott