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% 54 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 89 bins found. Bin 1 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 8 Assay one of these TagSNPs: RI-014094 A TagSNP from this bin will capture information on: UI-003497 UI-005383 UI-005659 UI-006248 UI-006267 RI-008347 RI-014094 UI-015898 Bin 2 Average minor allele frequency of sites in this bin: 29 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-017439 UI-017971 UI-018544 UI-019145 UI-019358 UI-019516 RI-019907 A TagSNP from this bin will capture information on: UI-017439 UI-017971 UI-018544 UI-019145 UI-019358 UI-019516 RI-019907 Bin 3 Average minor allele frequency of sites in this bin: 16 % # SNPs in this bin: 5 Assay one of these TagSNPs: RI-010987 RI-012836 RI-013124 RI-013272 UI-013834 A TagSNP from this bin will capture information on: RI-010987 RI-012836 RI-013124 RI-013272 UI-013834 Bin 4 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-010303 UI-013485 UI-014797 UI-015455 A TagSNP from this bin will capture information on: UI-010303 UI-013485 UI-014797 UI-015455 Bin 5 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-019980 UI-020348 UI-020352 A TagSNP from this bin will capture information on: UI-019980 UI-020348 UI-020352 Bin 6 Average minor allele frequency of sites in this bin: 42 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-000450 UF-000996 UF-001132 A TagSNP from this bin will capture information on: UF-000450 UF-000996 UF-001132 Bin 7 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-014970 A TagSNP from this bin will capture information on: UI-009932 RI-010930 UI-014970 Bin 8 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-016468 UN-019091 A TagSNP from this bin will capture information on: UI-016468 UN-019091 Bin 9 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-014183 UI-016981 A TagSNP from this bin will capture information on: UI-014183 UI-016981 Bin 10 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 2 Assay one of these TagSNPs: US-006779 US-007164 A TagSNP from this bin will capture information on: US-006779 US-007164 Bin 11 Average minor allele frequency of sites in this bin: 39 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-020628 UF-024693 A TagSNP from this bin will capture information on: UI-020628 UF-024693 Bin 12 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-008386 A TagSNP from this bin will capture information on: RI-008386 Bin 13 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001229 A TagSNP from this bin will capture information on: UF-001229 Bin 14 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-011999 A TagSNP from this bin will capture information on: RI-011999 Bin 15 Average minor allele frequency of sites in this bin: 15 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-014296 A TagSNP from this bin will capture information on: RI-014296 Bin 16 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-016897 A TagSNP from this bin will capture information on: UI-016897 Bin 17 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024023 A TagSNP from this bin will capture information on: UF-024023 Bin 18 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-012911 A TagSNP from this bin will capture information on: RI-012911 Bin 19 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-017696 A TagSNP from this bin will capture information on: UN-017696 Bin 20 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023288 A TagSNP from this bin will capture information on: UF-023288 Bin 21 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-018893 A TagSNP from this bin will capture information on: US-018893 Bin 22 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-014281 A TagSNP from this bin will capture information on: RI-014281 Bin 23 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000943 A TagSNP from this bin will capture information on: UF-000943 Bin 24 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000543 A TagSNP from this bin will capture information on: UF-000543 Bin 25 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024845 A TagSNP from this bin will capture information on: UF-024845 Bin 26 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024828 A TagSNP from this bin will capture information on: UF-024828 Bin 27 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024717 A TagSNP from this bin will capture information on: UF-024717 Bin 28 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024667 A TagSNP from this bin will capture information on: UF-024667 Bin 29 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024513 A TagSNP from this bin will capture information on: UF-024513 Bin 30 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024327 A TagSNP from this bin will capture information on: UF-024327 Bin 31 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024288 A TagSNP from this bin will capture information on: UF-024288 Bin 32 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024038 A TagSNP from this bin will capture information on: UF-024038 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023791 A TagSNP from this bin will capture information on: UF-023791 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023721 A TagSNP from this bin will capture information on: UF-023721 Bin 35 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023684 A TagSNP from this bin will capture information on: UF-023684 Bin 36 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023534 A TagSNP from this bin will capture information on: UF-023534 Bin 37 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023375 A TagSNP from this bin will capture information on: UF-023375 Bin 38 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1