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% 61 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 42 bins found. Bin 1 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 13 Assay one of these TagSNPs: UF-000138 RI-003460 UI-003875 UI-004462 RF-009737 RF-009856 RF-009888 RF-009966 UF-010179 UF-011502 RF-011885 RF-011970 RF-012257 A TagSNP from this bin will capture information on: UF-000138 RI-003460 UI-003875 UI-004462 RF-009737 RF-009856 RF-009888 RF-009966 UF-010179 UF-011502 RF-011885 RF-011970 RF-012257 Bin 2 Average minor allele frequency of sites in this bin: 7 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-001840 RI-003511 RT-007003 UT-007119 UT-007135 UF-009468 A TagSNP from this bin will capture information on: UI-001840 RI-003511 RT-007003 UT-007119 UT-007135 UF-009468 Bin 3 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-002648 UF-014271 UF-014305 RF-014447 UF-015030 A TagSNP from this bin will capture information on: UI-002648 UF-014271 UF-014305 RF-014447 UF-015030 Bin 4 Average minor allele frequency of sites in this bin: 16 % # SNPs in this bin: 5 Assay one of these TagSNPs: RI-003981 RI-004363 UF-010922 RF-012574 UF-013258 A TagSNP from this bin will capture information on: RI-003981 RI-004363 UF-010922 RF-012574 UF-013258 Bin 5 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-000200 RF-012714 RF-014722 A TagSNP from this bin will capture information on: UF-000200 RF-012714 RF-014722 Bin 6 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 3 Assay one of these TagSNPs: UF-000874 RI-003439 RF-009406 A TagSNP from this bin will capture information on: UF-000874 RI-003439 RF-009406 Bin 7 Average minor allele frequency of sites in this bin: 5 % # 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: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-002839 UI-004805 A TagSNP from this bin will capture information on: RI-002839 UI-004805 Bin 9 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-001673 RT-006830 A TagSNP from this bin will capture information on: UF-001673 RT-006830 Bin 10 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-003985 UN-006013 A TagSNP from this bin will capture information on: RI-003985 UN-006013 Bin 11 Average minor allele frequency of sites in this bin: 7 % # SNPs in this bin: 2 Assay one of these TagSNPs: UF-011075 UF-013795 A TagSNP from this bin will capture information on: UF-011075 UF-013795 Bin 12 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-002082 A TagSNP from this bin will capture information on: UI-002082 Bin 13 Average minor allele frequency of sites in this bin: 31 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001634 A TagSNP from this bin will capture information on: UF-001634 Bin 14 Average minor allele frequency of sites in this bin: 22 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-011353 A TagSNP from this bin will capture information on: UF-011353 Bin 15 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-007069 A TagSNP from this bin will capture information on: UT-007069 Bin 16 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009644 A TagSNP from this bin will capture information on: RF-009644 Bin 17 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-006510 A TagSNP from this bin will capture information on: UT-006510 Bin 18 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RT-007009 A TagSNP from this bin will capture information on: RT-007009 Bin 19 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-004514 A TagSNP from this bin will capture information on: UI-004514 Bin 20 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003348 A TagSNP from this bin will capture information on: RI-003348 Bin 21 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-014466 A TagSNP from this bin will capture information on: RF-014466 Bin 22 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-014211 A TagSNP from this bin will capture information on: UF-014211 Bin 23 Average minor allele frequency of sites in this bin: 2 % # 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: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-010632 A TagSNP from this bin will capture information on: RF-010632 Bin 25 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003239 A TagSNP from this bin will capture information on: RI-003239 Bin 26 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003015 A TagSNP from this bin will capture information on: RI-003015 Bin 27 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-014981 A TagSNP from this bin will capture information on: UF-014981 Bin 28 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-014794 A TagSNP from this bin will capture information on: UF-014794 Bin 29 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-012813 A TagSNP from this bin will capture information on: RF-012813 Bin 30 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-011327 A TagSNP from this bin will capture information on: UF-011327 Bin 31 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-009612 A TagSNP from this bin will capture information on: RF-009612 Bin 32 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-008993 A TagSNP from this bin will capture information on: RF-008993 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-007252 A TagSNP from this bin will capture information on: UT-007252 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RT-006954 A TagSNP from this bin will capture information on: RT-006954 Bin 35 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-004691 A TagSNP from this bin will capture information on: UI-004691 Bin 36 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004251 A TagSNP from this bin will capture information on: RI-004251 Bin 37 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003414 A TagSNP from this bin will capture information on: RI-003414 Bin 38 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003396 A TagSNP from this bin will capture information on: RI-003396 Bin 39 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003303 A TagSNP from this bin will capture information on: RI-003303 Bin 40 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001467 A TagSNP from this bin will capture information on: UF-001467 Bin 41 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-000554 A TagSNP from this bin will capture information on: RF-000554 Bin 42 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000527 A TagSNP from this bin will capture information on: UF-000527