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% 170 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 101 bins found. Bin 1 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 10 Assay one of these TagSNPs: RI-001563 UI-009222 RI-026023 RI-026182 UI-027299 RI-034075 UI-039589 UI-064314 UI-066459 UF-084997 A TagSNP from this bin will capture information on: RI-001563 UI-009222 RI-026023 RI-026182 UI-027299 RI-034075 UI-039589 UI-064314 UI-066459 UF-084997 Bin 2 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 9 Assay one of these TagSNPs: UI-004366 UI-004416 UI-008906 UI-009247 RI-016047 UI-016369 RI-017082 RI-017349 RI-026319 A TagSNP from this bin will capture information on: UI-004366 UI-004416 UI-008906 UI-009247 RI-016047 UI-016369 RI-017082 RI-017349 RI-026319 Bin 3 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-066470 A TagSNP from this bin will capture information on: RI-026600 RI-055224 RI-062033 UI-063548 UI-064082 RI-065044 RI-065352 UI-066470 Bin 4 Average minor allele frequency of sites in this bin: 42 % # SNPs in this bin: 7 Assay one of these TagSNPs: RI-062233 UI-063724 A TagSNP from this bin will capture information on: RI-062065 RI-062233 UI-063724 RI-064750 UI-066553 RI-067159 RI-067287 Bin 5 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 6 Assay one of these TagSNPs: RI-034376 A TagSNP from this bin will capture information on: UI-022077 RI-033715 RI-034108 RI-034376 UI-034790 UI-039297 Bin 6 Average minor allele frequency of sites in this bin: 9 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-001837 RI-002027 RI-002100 UI-002628 RI-004644 A TagSNP from this bin will capture information on: UI-001837 RI-002027 RI-002100 UI-002628 RI-004644 Bin 7 Average minor allele frequency of sites in this bin: 31 % # SNPs in this bin: 5 Assay one of these TagSNPs: RI-076098 RI-080486 UI-082302 A TagSNP from this bin will capture information on: RI-076098 UI-077215 RI-080486 UI-082302 UI-083932 Bin 8 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-004508 UI-005255 UI-008533 UI-067445 A TagSNP from this bin will capture information on: RI-004508 UI-005255 UI-008533 UI-067445 Bin 9 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-016656 UI-022382 RI-034354 RI-039723 A TagSNP from this bin will capture information on: RI-016656 UI-022382 RI-034354 RI-039723 Bin 10 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-022409 UI-064341 UI-065266 RI-080550 A TagSNP from this bin will capture information on: UI-022409 UI-064341 UI-065266 RI-080550 Bin 11 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-025263 RI-025460 UI-033326 RI-061550 A TagSNP from this bin will capture information on: RI-025263 RI-025460 UI-033326 RI-061550 Bin 12 Average minor allele frequency of sites in this bin: 16 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-063382 A TagSNP from this bin will capture information on: RI-062203 RI-062887 UI-063382 RI-067105 Bin 13 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-055335 RI-055599 UI-066582 UI-067700 A TagSNP from this bin will capture information on: RI-055335 RI-055599 UI-066582 UI-067700 Bin 14 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-027294 RI-032817 UI-033432 A TagSNP from this bin will capture information on: UI-027294 RI-032817 UI-033432 Bin 15 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-003343 RI-048128 US-081190 A TagSNP from this bin will capture information on: UI-003343 RI-048128 US-081190 Bin 16 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-026213 RI-055716 UI-082270 A TagSNP from this bin will capture information on: RI-026213 RI-055716 UI-082270 Bin 17 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-033713 UI-040009 RI-055614 A TagSNP from this bin will capture information on: RI-033713 UI-040009 RI-055614 Bin 18 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-034208 UI-064576 RI-065317 A TagSNP from this bin will capture information on: RI-034208 UI-064576 RI-065317 Bin 19 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-026967 UI-026968 RI-032885 A TagSNP from this bin will capture information on: UI-026967 UI-026968 RI-032885 Bin 20 Average minor allele frequency of sites in this bin: 36 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-075694 RI-080492 UI-083944 A TagSNP from this bin will capture information on: UI-075694 RI-080492 UI-083944 Bin 21 Average minor allele frequency of sites in this bin: 9 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-061435 UI-064144 UI-068949 A TagSNP from this bin will capture information on: RI-061435 UI-064144 UI-068949 Bin 22 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-026987 UI-069365 RI-077423 A TagSNP from this bin will capture information on: UI-026987 UI-069365 RI-077423 Bin 23 Average minor allele frequency of sites in this bin: 38 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-047237 A TagSNP from this bin will capture information on: RI-047237 RI-047951 UI-048348 Bin 24 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-017927 A TagSNP from this bin will capture information on: RI-017922 RI-017927 UI-084103 Bin 25 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-016574 RI-017420 A TagSNP from this bin will capture information on: RI-016574 RI-017420 Bin 26 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-016195 RI-016631 A TagSNP from this bin will capture information on: RI-016195 RI-016631 Bin 27 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-026203 RI-055345 A TagSNP from this bin will capture information on: RI-026203 RI-055345 Bin 28 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-026245 UI-064130 A TagSNP from this bin will capture information on: RI-026245 UI-064130 Bin 29 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-032982 RI-034443 A TagSNP from this bin will capture information on: UI-032982 RI-034443 Bin 30 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-047238 UI-068683 A TagSNP from this bin will capture information on: RI-047238 UI-068683 Bin 31 Average minor allele frequency of sites in this bin: 29 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-038743 UI-039413 A TagSNP from this bin will capture information on: UI-038743 UI-039413 Bin 32 Average minor allele frequency of sites in this bin: 36 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-003552 UI-009273 A TagSNP from this bin will capture information on: RI-003552 UI-009273 Bin 33 Average minor allele frequency of sites in this bin: 50 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026224 A TagSNP from this bin will capture information on: RI-026224 Bin 34 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-076198 A TagSNP from this bin will capture information on: UI-076198 Bin 35 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-082789 A TagSNP from this bin will capture information on: UI-082789 Bin 36 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017467 A TagSNP from this bin will capture information on: RI-017467 Bin 37 Average minor allele frequency of sites in this bin: 42 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-077608 A TagSNP from this bin will capture information on: RI-077608 Bin 38 Average minor allele frequency of sites in this bin: 39 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-008557 A TagSNP from this bin will capture information on: UI-008557 Bin 39 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-048063 A TagSNP from this bin will capture information on: RI-048063 Bin 40 Average minor allele frequency of sites in this bin: 28 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-008330 A TagSNP from this bin will capture information on: UI-008330 Bin 41 Average minor allele frequency of sites in this bin: 21 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-068451 A TagSNP from this bin will capture information on: UI-068451 Bin 42 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017864 A TagSNP from this bin will capture information on: RI-017864 Bin 43 Average minor allele frequency of sites in this bin: 18 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-075876 A TagSNP from this bin will capture information on: UI-075876 Bin 44 Average minor allele frequency of sites in this bin: 18 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-068932 A TagSNP from this bin will capture information on: UI-068932 Bin 45 Average minor allele frequency of sites in this bin: 18 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026174 A TagSNP from this bin will capture information on: RI-026174 Bin 46 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-070039 A TagSNP from this bin will capture information on: RI-070039 Bin 47 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-065623 A TagSNP from this bin will capture information on: RI-065623 Bin 48 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-069424 A TagSNP from this bin will capture information on: UI-069424 Bin 49 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-022140 A TagSNP from this bin will capture information on: UI-022140 Bin 50 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017081 A TagSNP from this bin will capture information on: RI-017081 Bin 51 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-075438 A TagSNP from this bin will capture information on: UI-075438 Bin 52 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-066220 A TagSNP from this bin will capture information on: UI-066220 Bin 53 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-048346 A TagSNP from this bin will capture information on: UI-048346 Bin 54 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026162 A TagSNP from this bin will capture information on: RI-026162 Bin 55 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-075910 A TagSNP from this bin will capture information on: RI-075910 Bin 56 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-047474 A TagSNP from this bin will capture information on: RI-047474 Bin 57 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-038731 A TagSNP from this bin will capture information on: UI-038731 Bin 58 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-035002 A TagSNP from this bin will capture information on: RI-035002 Bin 59 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-034970 A TagSNP from this bin will capture information on: RI-034970 Bin 60 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026233 A TagSNP from this bin will capture information on: RI-026233 Bin 61 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-063277 A TagSNP from this bin will capture information on: RI-063277 Bin 62 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-034992 A TagSNP from this bin will capture information on: RI-034992 Bin 63 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026389 A TagSNP from this bin will capture information on: RI-026389 Bin 64 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-025273 A TagSNP from this bin will capture information on: RI-025273 Bin 65 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-025220 A TagSNP from this bin will capture information on: RI-025220 Bin 66 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017464 A TagSNP from this bin will capture information on: RI-017464 Bin 67 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-080913 A TagSNP from this bin will capture information on: UI-080913 Bin 68 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-075724 A TagSNP from this bin will capture information on: UI-075724 Bin 69 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-026193 A TagSNP from this bin will capture information on: RI-026193 Bin 70 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-002591 A TagSNP from this bin will capture information on: RI-002591 Bin 71 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-001954 A TagSNP from this bin will capture information on: RI-001954 Bin 72 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-065066 A TagSNP from this bin will capture information on: RI-065066 Bin 73 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-055960 A TagSNP from this bin will capture information on: RI-055960 Bin 74 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-033827 A TagSNP from this bin will capture information on: RI-033827 Bin 75 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-025437 A TagSNP from this bin will capture information on: RI-025437 Bin 76 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-022732 A TagSNP from this bin will capture information on: RI-022732 Bin 77 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-009007 A TagSNP from this bin will capture information on: UI-009007 Bin 78 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-004438 A TagSNP from this bin will capture information on: UI-004438 Bin 79 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-004196 A TagSNP from this bin will capture information on: UI-004196 Bin 80 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-084970 A TagSNP from this bin will capture information on: UF-084970 Bin 81 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-084761 A TagSNP from this bin will capture information on: UT-084761 Bin 82 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-082291 A TagSNP from this bin will capture information on: UI-082291 Bin 83 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-081594 A TagSNP from this bin will capture information on: UI-081594 Bin 84 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-075049 A TagSNP from this bin will capture information on: UI-075049 Bin 85 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-069853 A TagSNP from this bin will capture information on: UI-069853 Bin 86 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1