LDSelect output LDSelect analyzes the patterns of linkage disequilibrium between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r^2. At each round, the binning algorithm identifies the single SNP which exceeds threshold r^2 with the maximum number of other SNPs, and sets this set of SNPs as a bin. Then each SNP within the bin is analyzed to determine whether it exceeds threshold r^2 with all other SNPs in the bin. All SNPs in a bin that meet this criterion are designated as TagSNPs. Only one TagSNP needs to be typed per bin. The sequence context for each SNP is indicated by a two letter code preceeding the SNP reference sequence position. The first position of the code indicates whether the sequence context is: (U)nique sequence or (R)epeat containing sequence. This information is important because design genotyping assays is generally easier for unique sequences. The second position in the code provides information on the genomic context: (F)lanking region, 5' or 3' U(T)R, (I)ntron, (S)ynonymous cSNP, or (N)onsynonymous cSNP. As an example, UN-005467 is in a unique sequence context, is a non-synonymous SNP, and is at position 005467 in the reference sequence of the gene. Results from LDSelect are sorted by bin size, from largest to smallest. The smallest bins usually contain a single SNP, which indicates that they are not in LD at the required threshold with any other SNP, and these are sorted by allele frequency at the end of file. SNP minor allele frequency threshold 0% 81 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 140 bins found. Bin 1 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 18 Assay one of these TagSNPs: RI-062065 RI-062203 RI-062233 RI-062887 UI-063382 UI-063724 UI-066553 RI-067105 RI-067159 RI-067287 UI-068451 A TagSNP from this bin will capture information on: RI-047237 RI-047951 UI-048346 UI-048348 RI-062065 RI-062203 RI-062233 RI-062887 UI-063382 UI-063724 RI-064750 UI-066553 RI-067105 RI-067159 RI-067287 UI-068451 UI-068683 RI-070039 Bin 2 Average minor allele frequency of sites in this bin: 18 % # SNPs in this bin: 10 Assay one of these TagSNPs: UI-075694 UI-075876 UI-076198 UI-077215 RI-077608 RI-080492 RI-080550 UI-080913 UI-082789 UI-083944 A TagSNP from this bin will capture information on: UI-075694 UI-075876 UI-076198 UI-077215 RI-077608 RI-080492 RI-080550 UI-080913 UI-082789 UI-083944 Bin 3 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-008330 UI-008557 A TagSNP from this bin will capture information on: RI-003552 UI-008330 UI-008557 UI-009273 RI-017864 Bin 4 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-008532 RI-026193 UI-026935 UI-034670 A TagSNP from this bin will capture information on: UI-008532 RI-026193 UI-026935 UI-034670 Bin 5 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-026182 RI-034992 RI-065195 UF-084970 A TagSNP from this bin will capture information on: RI-026182 RI-034992 RI-065195 UF-084970 Bin 6 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-025273 RI-026389 UI-026967 UI-026968 A TagSNP from this bin will capture information on: RI-025273 RI-026389 UI-026967 UI-026968 Bin 7 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-001955 UI-039230 UT-047582 A TagSNP from this bin will capture information on: RI-001955 UI-039230 UT-047582 Bin 8 Average minor allele frequency of sites in this bin: 9 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-003343 RI-017372 RI-017467 A TagSNP from this bin will capture information on: UI-003343 RI-017372 RI-017467 Bin 9 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-026188 A TagSNP from this bin will capture information on: RI-026188 RI-061550 UI-075049 Bin 10 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-017922 RI-017927 A TagSNP from this bin will capture information on: RI-017922 RI-017927 Bin 11 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-034208 UI-039413 A TagSNP from this bin will capture information on: RI-034208 UI-039413 Bin 12 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-025263 RI-025460 A TagSNP from this bin will capture information on: RI-025263 RI-025460 Bin 13 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-026174 UI-068932 A TagSNP from this bin will capture information on: RI-026174 UI-068932 Bin 14 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UN-067581 RI-075910 A TagSNP from this bin will capture information on: UN-067581 RI-075910 Bin 15 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-081594 UT-084761 A TagSNP from this bin will capture information on: UI-081594 UT-084761 Bin 16 Average minor allele frequency of sites in this bin: 15 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-032885 UI-038743 A TagSNP from this bin will capture information on: RI-032885 UI-038743 Bin 17 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-022409 A TagSNP from this bin will capture information on: UI-022409 Bin 18 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-047238 A TagSNP from this bin will capture information on: RI-047238 Bin 19 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-048063 A TagSNP from this bin will capture information on: RI-048063 Bin 20 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-047875 A TagSNP from this bin will capture information on: RI-047875 Bin 21 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-033827 A TagSNP from this bin will capture information on: RI-033827 Bin 22 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026023 A TagSNP from this bin will capture information on: RI-026023 Bin 23 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-082291 A TagSNP from this bin will capture information on: UI-082291 Bin 24 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-069853 A TagSNP from this bin will capture information on: UI-069853 Bin 25 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-039357 A TagSNP from this bin will capture information on: UI-039357 Bin 26 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-032832 A TagSNP from this bin will capture information on: RI-032832 Bin 27 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-022987 A TagSNP from this bin will capture information on: RI-022987 Bin 28 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-009371 A TagSNP from this bin will capture information on: UI-009371 Bin 29 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000615 A TagSNP from this bin will capture information on: UF-000615 Bin 30 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-084997 A TagSNP from this bin will capture information on: UF-084997 Bin 31 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-084103 A TagSNP from this bin will capture information on: UI-084103 Bin 32 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-083932 A TagSNP from this bin will capture information on: UI-083932 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-082302 A TagSNP from this bin will capture information on: UI-082302 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-082270 A TagSNP from this bin will capture information on: UI-082270 Bin 35 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1