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% 159 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 94 bins found. Bin 1 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 11 Assay one of these TagSNPs: UI-007761 UN-007960 A TagSNP from this bin will capture information on: UI-003199 UI-007761 UN-007960 UI-012030 RI-014170 RI-014176 RI-018661 UN-019218 UI-024103 RI-027730 US-033528 Bin 2 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-002404 RI-007518 UI-008691 RI-014625 UI-016225 UI-018343 RI-025594 A TagSNP from this bin will capture information on: UI-002404 RI-007518 UI-008691 RI-014625 UI-016225 UI-018343 RI-025594 Bin 3 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-006519 UI-006579 RI-007651 RI-015699 UI-017049 RI-027598 UI-032921 A TagSNP from this bin will capture information on: UI-006519 UI-006579 RI-007651 RI-015699 UI-017049 RI-027598 UI-032921 Bin 4 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-019243 RI-019745 RI-024469 UI-025246 UI-025288 RI-025456 RI-027745 A TagSNP from this bin will capture information on: UI-019243 RI-019745 RI-024469 UI-025246 UI-025288 RI-025456 RI-027745 Bin 5 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-030761 UI-031661 UI-031796 UN-036530 UN-039043 US-041375 A TagSNP from this bin will capture information on: UI-030761 UI-031661 UI-031796 UN-036530 UN-039043 US-041375 Bin 6 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-002289 US-003553 RI-005977 UI-012482 UI-023352 UI-028186 A TagSNP from this bin will capture information on: UI-002289 US-003553 RI-005977 UI-012482 UI-023352 UI-028186 Bin 7 Average minor allele frequency of sites in this bin: 15 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-009333 RI-018677 RI-024900 US-036099 US-036708 A TagSNP from this bin will capture information on: UI-009333 RI-018677 RI-024900 US-036099 US-036708 Bin 8 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-012947 RI-016796 UN-017533 A TagSNP from this bin will capture information on: UI-006138 UI-012947 RI-016796 UN-017533 UI-031117 Bin 9 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-028536 UI-028869 UN-037379 UN-043622 A TagSNP from this bin will capture information on: RI-028536 UI-028869 UN-037379 UN-043622 Bin 10 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-005992 UI-013162 UI-013163 RI-029319 A TagSNP from this bin will capture information on: RI-005992 UI-013162 UI-013163 RI-029319 Bin 11 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-010294 RI-025534 RI-027156 US-041726 A TagSNP from this bin will capture information on: UI-010294 RI-025534 RI-027156 US-041726 Bin 12 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-029318 UI-033055 UN-036058 UT-044481 A TagSNP from this bin will capture information on: RI-029318 UI-033055 UN-036058 UT-044481 Bin 13 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-006035 UI-009566 UN-013545 UI-016184 A TagSNP from this bin will capture information on: RI-006035 UI-009566 UN-013545 UI-016184 Bin 14 Average minor allele frequency of sites in this bin: 7 % # SNPs in this bin: 4 Assay one of these TagSNPs: UF-001800 UI-002730 UI-003957 UI-004160 A TagSNP from this bin will capture information on: UF-001800 UI-002730 UI-003957 UI-004160 Bin 15 Average minor allele frequency of sites in this bin: 26 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-007387 UI-008293 RI-013322 UI-017860 A TagSNP from this bin will capture information on: UI-007387 UI-008293 RI-013322 UI-017860 Bin 16 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-006704 RI-015660 UI-017187 US-039900 A TagSNP from this bin will capture information on: RI-006704 RI-015660 UI-017187 US-039900 Bin 17 Average minor allele frequency of sites in this bin: 11 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-006551 UI-008759 UI-013903 UI-017100 A TagSNP from this bin will capture information on: UI-006551 UI-008759 UI-013903 UI-017100 Bin 18 Average minor allele frequency of sites in this bin: 9 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-024581 UI-025245 RI-027904 US-038167 A TagSNP from this bin will capture information on: RI-024581 UI-025245 RI-027904 US-038167 Bin 19 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-022763 UI-031873 UN-038998 A TagSNP from this bin will capture information on: UI-022763 UI-031873 UN-038998 Bin 20 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-008534 RI-014515 UI-017372 A TagSNP from this bin will capture information on: UI-008534 RI-014515 UI-017372 Bin 21 Average minor allele frequency of sites in this bin: 11 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-030006 UI-042651 UN-043418 A TagSNP from this bin will capture information on: RI-030006 UI-042651 UN-043418 Bin 22 Average minor allele frequency of sites in this bin: 9 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-006467 UI-009283 UN-017986 A TagSNP from this bin will capture information on: RI-006467 UI-009283 UN-017986 Bin 23 Average minor allele frequency of sites in this bin: 24 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-023571 UI-031359 UI-042343 A TagSNP from this bin will capture information on: UI-023571 UI-031359 UI-042343 Bin 24 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-041520 UI-041572 UN-044060 A TagSNP from this bin will capture information on: UI-041520 UI-041572 UN-044060 Bin 25 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-022594 UI-023533 A TagSNP from this bin will capture information on: UI-022594 UI-023533 Bin 26 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-002996 RI-029184 A TagSNP from this bin will capture information on: UI-002996 RI-029184 Bin 27 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-004795 UN-023011 A TagSNP from this bin will capture information on: UI-004795 UN-023011 Bin 28 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-006226 UI-032063 A TagSNP from this bin will capture information on: UI-006226 UI-032063 Bin 29 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-006514 UI-011518 A TagSNP from this bin will capture information on: UI-006514 UI-011518 Bin 30 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-020799 UN-030536 A TagSNP from this bin will capture information on: UI-020799 UN-030536 Bin 31 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-027610 US-043393 A TagSNP from this bin will capture information on: RI-027610 US-043393 Bin 32 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-029130 RI-029131 A TagSNP from this bin will capture information on: RI-029130 RI-029131 Bin 33 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-015272 RI-015273 A TagSNP from this bin will capture information on: RI-015272 RI-015273 Bin 34 Average minor allele frequency of sites in this bin: 11 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-001433 UN-004994 A TagSNP from this bin will capture information on: UF-001433 UN-004994 Bin 35 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-000675 UI-005255 A TagSNP from this bin will capture information on: UF-000675 UI-005255 Bin 36 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-006703 RI-029820 A TagSNP from this bin will capture information on: RI-006703 RI-029820 Bin 37 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-010968 UN-040076 A TagSNP from this bin will capture information on: UI-010968 UN-040076 Bin 38 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001684 A TagSNP from this bin will capture information on: UF-001684 Bin 39 Average minor allele frequency of sites in this bin: 31 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-027395 A TagSNP from this bin will capture information on: RI-027395 Bin 40 Average minor allele frequency of sites in this bin: 19 % # SNPs in this bin: 1 Assay one of these TagSNPs: UX-002111 A TagSNP from this bin will capture information on: UX-002111 Bin 41 Average minor allele frequency of sites in this bin: 18 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-043150 A TagSNP from this bin will capture information on: UN-043150 Bin 42 Average minor allele frequency of sites in this bin: 18 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-029242 A TagSNP from this bin will capture information on: RI-029242 Bin 43 Average minor allele frequency of sites in this bin: 16 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-022693 A TagSNP from this bin will capture information on: UI-022693 Bin 44 Average minor allele frequency of sites in this bin: 16 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001112 A TagSNP from this bin will capture information on: UF-001112 Bin 45 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-039864 A TagSNP from this bin will capture information on: US-039864 Bin 46 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021689 A TagSNP from this bin will capture information on: RI-021689 Bin 47 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-029236 A TagSNP from this bin will capture information on: RI-029236 Bin 48 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-003753 A TagSNP from this bin will capture information on: UI-003753 Bin 49 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-037311 A TagSNP from this bin will capture information on: US-037311 Bin 50 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-028524 A TagSNP from this bin will capture information on: RI-028524 Bin 51 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021613 A TagSNP from this bin will capture information on: RI-021613 Bin 52 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013734 A TagSNP from this bin will capture information on: UI-013734 Bin 53 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-003376 A TagSNP from this bin will capture information on: UI-003376 Bin 54 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-002235 A TagSNP from this bin will capture information on: UI-002235 Bin 55 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-001962 A TagSNP from this bin will capture information on: UT-001962 Bin 56 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-000063 A TagSNP from this bin will capture information on: RF-000063 Bin 57 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-031665 A TagSNP from this bin will capture information on: UI-031665 Bin 58 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-029516 A TagSNP from this bin will capture information on: UN-029516 Bin 59 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1