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% 102 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 69 bins found. Bin 1 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-008785 UI-010213 RI-012332 UI-014877 UI-014983 A TagSNP from this bin will capture information on: UF-000835 UI-006248 UI-008785 UI-010213 RI-012332 RI-012808 UI-014877 UI-014983 Bin 2 Average minor allele frequency of sites in this bin: 44 % # SNPs in this bin: 6 Assay one of these TagSNPs: RI-010987 RI-012836 RI-013124 RI-013272 UI-013834 UI-014970 A TagSNP from this bin will capture information on: RI-010987 RI-012836 RI-013124 RI-013272 UI-013834 UI-014970 Bin 3 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 5 Assay one of these TagSNPs: UF-001339 UF-001345 UN-018400 UF-023791 UF-024288 A TagSNP from this bin will capture information on: UF-001339 UF-001345 UN-018400 UF-023791 UF-024288 Bin 4 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UF-000823 UI-002493 UI-008275 UI-016499 A TagSNP from this bin will capture information on: UF-000823 UI-002493 UI-008275 UI-016499 Bin 5 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-019773 UF-023534 UF-024038 UF-024327 A TagSNP from this bin will capture information on: RI-019773 UF-023534 UF-024038 UF-024327 Bin 6 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-017433 RI-019772 UI-020819 UF-023375 A TagSNP from this bin will capture information on: UI-017433 RI-019772 UI-020819 UF-023375 Bin 7 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-018544 UI-019358 RI-019907 A TagSNP from this bin will capture information on: UI-018544 UI-019358 RI-019907 Bin 8 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-001023 UI-002226 RI-012351 A TagSNP from this bin will capture information on: UF-001023 UI-002226 RI-012351 Bin 9 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-001062 UF-023721 UF-024845 A TagSNP from this bin will capture information on: UF-001062 UF-023721 UF-024845 Bin 10 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-005410 RI-013244 US-021449 A TagSNP from this bin will capture information on: UI-005410 RI-013244 US-021449 Bin 11 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-015534 UI-017041 UI-020961 A TagSNP from this bin will capture information on: UI-015534 UI-017041 UI-020961 Bin 12 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-019258 UI-021741 UI-021742 A TagSNP from this bin will capture information on: UI-019258 UI-021741 UI-021742 Bin 13 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 3 Assay one of these TagSNPs: US-006779 UN-007164 RI-008386 A TagSNP from this bin will capture information on: US-006779 UN-007164 RI-008386 Bin 14 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-014797 A TagSNP from this bin will capture information on: RI-008347 UI-010303 UI-014797 Bin 15 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-005659 UI-006267 A TagSNP from this bin will capture information on: UI-005659 UI-006267 Bin 16 Average minor allele frequency of sites in this bin: 15 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-000996 UF-001132 A TagSNP from this bin will capture information on: UF-000996 UF-001132 Bin 17 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-000479 UI-006237 A TagSNP from this bin will capture information on: UF-000479 UI-006237 Bin 18 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-000985 UI-017749 A TagSNP from this bin will capture information on: UF-000985 UI-017749 Bin 19 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-008860 UF-024667 A TagSNP from this bin will capture information on: UI-008860 UF-024667 Bin 20 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-013384 UI-014184 A TagSNP from this bin will capture information on: RI-013384 UI-014184 Bin 21 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-017797 UI-018581 A TagSNP from this bin will capture information on: UI-017797 UI-018581 Bin 22 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-004887 UI-008149 A TagSNP from this bin will capture information on: UI-004887 UI-008149 Bin 23 Average minor allele frequency of sites in this bin: 29 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-017971 UI-019516 A TagSNP from this bin will capture information on: UI-017971 UI-019516 Bin 24 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-017439 A TagSNP from this bin will capture information on: UI-017439 Bin 25 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-015898 A TagSNP from this bin will capture information on: UI-015898 Bin 26 Average minor allele frequency of sites in this bin: 39 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000450 A TagSNP from this bin will capture information on: UF-000450 Bin 27 Average minor allele frequency of sites in this bin: 33 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-014094 A TagSNP from this bin will capture information on: RI-014094 Bin 28 Average minor allele frequency of sites in this bin: 33 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-009932 A TagSNP from this bin will capture information on: UI-009932 Bin 29 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-018173 A TagSNP from this bin will capture information on: UI-018173 Bin 30 Average minor allele frequency of sites in this bin: 25 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-016665 A TagSNP from this bin will capture information on: RI-016665 Bin 31 Average minor allele frequency of sites in this bin: 25 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-011034 A TagSNP from this bin will capture information on: RI-011034 Bin 32 Average minor allele frequency of sites in this bin: 23 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-005383 A TagSNP from this bin will capture information on: UI-005383 Bin 33 Average minor allele frequency of sites in this bin: 22 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013485 A TagSNP from this bin will capture information on: UI-013485 Bin 34 Average minor allele frequency of sites in this bin: 16 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-018999 A TagSNP from this bin will capture information on: UI-018999 Bin 35 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-021964 A TagSNP from this bin will capture information on: US-021964 Bin 36 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-020628 A TagSNP from this bin will capture information on: UI-020628 Bin 37 Average minor allele frequency of sites in this bin: 11 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-015455 A TagSNP from this bin will capture information on: UI-015455 Bin 38 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-016255 A TagSNP from this bin will capture information on: UI-016255 Bin 39 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-014281 A TagSNP from this bin will capture information on: RI-014281 Bin 40 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013644 A TagSNP from this bin will capture information on: UI-013644 Bin 41 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-004609 A TagSNP from this bin will capture information on: UN-004609 Bin 42 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024513 A TagSNP from this bin will capture information on: UF-024513 Bin 43 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-019145 A TagSNP from this bin will capture information on: UI-019145 Bin 44 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-008148 A TagSNP from this bin will capture information on: UI-008148 Bin 45 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024693 A TagSNP from this bin will capture information on: UF-024693 Bin 46 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-016897 A TagSNP from this bin will capture information on: UI-016897 Bin 47 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-014296 A TagSNP from this bin will capture information on: RI-014296 Bin 48 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024828 A TagSNP from this bin will capture information on: UF-024828 Bin 49 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024717 A TagSNP from this bin will capture information on: UF-024717 Bin 50 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023684 A TagSNP from this bin will capture information on: UF-023684 Bin 51 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000789 A TagSNP from this bin will capture information on: UF-000789 Bin 52 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 53 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-024023 A TagSNP from this bin will capture information on: UF-024023 Bin 54 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-023288 A TagSNP from this bin will capture information on: UF-023288 Bin 55 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-020352 A TagSNP from this bin will capture information on: UI-020352 Bin 56 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-020348 A TagSNP from this bin will capture information on: UI-020348 Bin 57 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-019980 A TagSNP from this bin will capture information on: UI-019980 Bin 58 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1