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% 49 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 47 bins found. Bin 1 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 9 Assay one of these TagSNPs: RI-003439 RF-009406 UF-013795 RF-014447 UF-015030 A TagSNP from this bin will capture information on: UF-000874 UI-002648 RI-003439 RF-009406 UF-013795 UF-014271 UF-014305 RF-014447 UF-015030 Bin 2 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 7 Assay one of these TagSNPs: UI-001840 RI-003511 UT-006510 RT-007003 UT-007119 UT-007135 UF-009468 A TagSNP from this bin will capture information on: UI-001840 RI-003511 UT-006510 RT-007003 UT-007119 UT-007135 UF-009468 Bin 3 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 4 Assay one of these TagSNPs: RT-006954 RF-009612 UF-011327 UF-014981 A TagSNP from this bin will capture information on: RT-006954 RF-009612 UF-011327 UF-014981 Bin 4 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UF-000527 RF-000554 UI-004691 RF-012813 A TagSNP from this bin will capture information on: UF-000527 RF-000554 UI-004691 RF-012813 Bin 5 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 4 Assay one of these TagSNPs: UF-000200 RI-003985 RF-012714 RF-014722 A TagSNP from this bin will capture information on: UF-000200 RI-003985 RF-012714 RF-014722 Bin 6 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-004363 UF-010922 RF-012574 A TagSNP from this bin will capture information on: RI-004363 UF-010922 RF-012574 Bin 7 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-000710 UN-001771 RF-014548 A TagSNP from this bin will capture information on: UF-000710 UN-001771 RF-014548 Bin 8 Average minor allele frequency of sites in this bin: 28 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-002082 UT-007069 UF-011353 A TagSNP from this bin will capture information on: UI-002082 UT-007069 UF-011353 Bin 9 Average minor allele frequency of sites in this bin: 34 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-003981 UF-013258 A TagSNP from this bin will capture information on: RI-003981 UF-013258 Bin 10 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001634 A TagSNP from this bin will capture information on: UF-001634 Bin 11 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-011075 A TagSNP from this bin will capture information on: UF-011075 Bin 12 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003303 A TagSNP from this bin will capture information on: RI-003303 Bin 13 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004251 A TagSNP from this bin will capture information on: RI-004251 Bin 14 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001467 A TagSNP from this bin will capture information on: UF-001467 Bin 15 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-008993 A TagSNP from this bin will capture information on: RF-008993 Bin 16 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-014794 A TagSNP from this bin will capture information on: UF-014794 Bin 17 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-007252 A TagSNP from this bin will capture information on: UT-007252 Bin 18 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003414 A TagSNP from this bin will capture information on: RI-003414 Bin 19 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003396 A TagSNP from this bin will capture information on: RI-003396 Bin 20 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-014466 A TagSNP from this bin will capture information on: RF-014466 Bin 21 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-014211 A TagSNP from this bin will capture information on: UF-014211 Bin 22 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-012257 A TagSNP from this bin will capture information on: RF-012257 Bin 23 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-012161 A TagSNP from this bin will capture information on: RF-012161 Bin 24 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-011970 A TagSNP from this bin will capture information on: RF-011970 Bin 25 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-011885 A TagSNP from this bin will capture information on: RF-011885 Bin 26 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-011502 A TagSNP from this bin will capture information on: UF-011502 Bin 27 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-010632 A TagSNP from this bin will capture information on: RF-010632 Bin 28 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-010179 A TagSNP from this bin will capture information on: UF-010179 Bin 29 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009966 A TagSNP from this bin will capture information on: RF-009966 Bin 30 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009888 A TagSNP from this bin will capture information on: RF-009888 Bin 31 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009856 A TagSNP from this bin will capture information on: RF-009856 Bin 32 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009737 A TagSNP from this bin will capture information on: RF-009737 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009644 A TagSNP from this bin will capture information on: RF-009644 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RT-007009 A TagSNP from this bin will capture information on: RT-007009 Bin 35 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RT-006830 A TagSNP from this bin will capture information on: RT-006830 Bin 36 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1