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% 79 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 148 bins found. Bin 1 Average minor allele frequency of sites in this bin: 48 % # SNPs in this bin: 9 Assay one of these TagSNPs: UI-009333 RI-018677 RI-024900 A TagSNP from this bin will capture information on: RI-006467 UI-009283 UI-009333 UN-017986 RI-018677 RI-024900 RI-029236 US-036099 US-036708 Bin 2 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-007387 UI-008293 RI-013322 UI-017860 UI-022594 UI-023533 RI-029242 A TagSNP from this bin will capture information on: UI-007387 UI-008293 RI-013322 UI-017860 UI-022594 UI-023533 RI-029242 Bin 3 Average minor allele frequency of sites in this bin: 24 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-023571 RI-028536 A TagSNP from this bin will capture information on: UI-023571 RI-028536 UI-028869 UI-031359 UN-037379 UI-042343 UN-043622 Bin 4 Average minor allele frequency of sites in this bin: 19 % # SNPs in this bin: 5 Assay one of these TagSNPs: RI-021689 RI-027156 UI-031665 UI-041520 UN-043150 A TagSNP from this bin will capture information on: RI-021689 RI-027156 UI-031665 UI-041520 UN-043150 Bin 5 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-006355 UI-012489 UN-038707 UN-043790 A TagSNP from this bin will capture information on: RI-006355 UI-012489 UN-038707 UN-043790 Bin 6 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-018435 UI-028274 UI-028362 UN-040564 A TagSNP from this bin will capture information on: RI-018435 UI-028274 UI-028362 UN-040564 Bin 7 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-001684 UI-003376 UI-005255 A TagSNP from this bin will capture information on: UF-001684 UI-003376 UI-005255 Bin 8 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-004441 RI-014731 RI-025856 A TagSNP from this bin will capture information on: RI-004441 RI-014731 RI-025856 Bin 9 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-029292 UI-033338 UN-039835 A TagSNP from this bin will capture information on: RI-029292 UI-033338 UN-039835 Bin 10 Average minor allele frequency of sites in this bin: 37 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-001433 UX-002111 UN-004994 A TagSNP from this bin will capture information on: UF-001433 UX-002111 UN-004994 Bin 11 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-001112 UI-003753 A TagSNP from this bin will capture information on: UF-001112 UI-003753 Bin 12 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-027395 UI-031117 A TagSNP from this bin will capture information on: RI-027395 UI-031117 Bin 13 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-014336 RI-029910 A TagSNP from this bin will capture information on: RI-014336 RI-029910 Bin 14 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RF-000063 UI-017370 A TagSNP from this bin will capture information on: RF-000063 UI-017370 Bin 15 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-010968 UI-020804 A TagSNP from this bin will capture information on: UI-010968 UI-020804 Bin 16 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-015590 UI-041101 A TagSNP from this bin will capture information on: RI-015590 UI-041101 Bin 17 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-025874 UN-030490 A TagSNP from this bin will capture information on: RI-025874 UN-030490 Bin 18 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: US-039294 UN-042991 A TagSNP from this bin will capture information on: US-039294 UN-042991 Bin 19 Average minor allele frequency of sites in this bin: 19 % # 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 20 Average minor allele frequency of sites in this bin: 15 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-040076 A TagSNP from this bin will capture information on: UN-040076 Bin 21 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-024542 A TagSNP from this bin will capture information on: RI-024542 Bin 22 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-044050 A TagSNP from this bin will capture information on: UN-044050 Bin 23 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-006896 A TagSNP from this bin will capture information on: RI-006896 Bin 24 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-029308 A TagSNP from this bin will capture information on: RI-029308 Bin 25 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-023087 A TagSNP from this bin will capture information on: US-023087 Bin 26 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-019184 A TagSNP from this bin will capture information on: UN-019184 Bin 27 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-006023 A TagSNP from this bin will capture information on: RI-006023 Bin 28 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-028188 A TagSNP from this bin will capture information on: UI-028188 Bin 29 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-034904 A TagSNP from this bin will capture information on: UN-034904 Bin 30 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-028453 A TagSNP from this bin will capture information on: RI-028453 Bin 31 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-024283 A TagSNP from this bin will capture information on: RI-024283 Bin 32 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-012182 A TagSNP from this bin will capture information on: UI-012182 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-044481 A TagSNP from this bin will capture information on: UT-044481 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1