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% 128 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 178 bins found. Bin 1 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 25 Assay one of these TagSNPs: RI-004381 UI-013802 RI-019050 RI-019070 RI-019262 UI-019487 UI-019592 UI-019610 UI-019750 UI-020018 UI-020371 UI-021705 UI-021936 UI-022531 A TagSNP from this bin will capture information on: RI-004381 UI-013802 UI-018142 RI-019050 RI-019070 RI-019262 UI-019487 UI-019592 UI-019610 UI-019750 UI-020018 UI-020371 UI-021705 UI-021936 UI-022531 UI-023225 UI-023476 UI-024446 RI-024552 UI-024708 UI-025525 RI-026623 RI-026808 UI-028640 UI-030288 Bin 2 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 23 Assay one of these TagSNPs: UI-036721 UI-037040 RI-037783 RI-037795 RI-037933 UI-038259 UI-038369 UI-039615 UI-039650 UI-039731 UI-039884 UI-039922 UI-040040 UI-040140 UI-041111 UI-041696 UI-041840 UI-042040 UI-042221 A TagSNP from this bin will capture information on: UI-033986 UI-036635 UI-036721 UI-037040 RI-037783 RI-037795 RI-037933 UI-038259 UI-038369 UI-039615 UI-039650 UI-039731 UI-039884 UI-039922 UI-040040 UI-040140 UI-041111 RI-041499 UI-041575 UI-041696 UI-041840 UI-042040 UI-042221 Bin 3 Average minor allele frequency of sites in this bin: 32 % # SNPs in this bin: 16 Assay one of these TagSNPs: UI-008263 RI-008897 RI-009185 UI-010243 UI-011161 RI-011974 UI-012890 UI-013005 UI-013489 UI-013578 UI-013973 UI-014051 UI-014148 UI-014359 UI-017146 UI-017272 A TagSNP from this bin will capture information on: UI-008263 RI-008897 RI-009185 UI-010243 UI-011161 RI-011974 UI-012890 UI-013005 UI-013489 UI-013578 UI-013973 UI-014051 UI-014148 UI-014359 UI-017146 UI-017272 Bin 4 Average minor allele frequency of sites in this bin: 25 % # SNPs in this bin: 14 Assay one of these TagSNPs: RF-000478 UF-001568 RF-001896 RF-001993 UI-003529 UI-004052 UI-004205 UI-006203 UI-012109 UI-014679 UI-015373 UI-017785 UI-019982 UI-023327 A TagSNP from this bin will capture information on: RF-000478 UF-001568 RF-001896 RF-001993 UI-003529 UI-004052 UI-004205 UI-006203 UI-012109 UI-014679 UI-015373 UI-017785 UI-019982 UI-023327 Bin 5 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-035440 RI-037609 UI-039904 UI-040903 UI-042069 UI-042810 UI-042866 UI-043481 A TagSNP from this bin will capture information on: UI-035440 RI-037609 UI-039904 UI-040903 UI-042069 UI-042810 UI-042866 UI-043481 Bin 6 Average minor allele frequency of sites in this bin: 39 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-008266 UI-009205 RI-015687 UI-022772 A TagSNP from this bin will capture information on: UI-008266 UI-009205 RI-015687 UI-022772 Bin 7 Average minor allele frequency of sites in this bin: 21 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-033401 UI-034778 A TagSNP from this bin will capture information on: UI-033401 UI-034778 UI-040348 UI-042559 Bin 8 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 3 Assay one of these TagSNPs: RF-002186 UI-007526 UI-019387 A TagSNP from this bin will capture information on: RF-002186 UI-007526 UI-019387 Bin 9 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-013214 UI-017938 UI-032012 A TagSNP from this bin will capture information on: UI-013214 UI-017938 UI-032012 Bin 10 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-036099 UI-036179 A TagSNP from this bin will capture information on: UI-036099 UI-036179 Bin 11 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: US-046905 UT-047360 A TagSNP from this bin will capture information on: US-046905 UT-047360 Bin 12 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-024522 UI-025158 A TagSNP from this bin will capture information on: RI-024522 UI-025158 Bin 13 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-013590 UI-024347 A TagSNP from this bin will capture information on: UI-013590 UI-024347 Bin 14 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-037858 UI-044676 A TagSNP from this bin will capture information on: UI-037858 UI-044676 Bin 15 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-046416 A TagSNP from this bin will capture information on: US-046416 Bin 16 Average minor allele frequency of sites in this bin: 34 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047009 A TagSNP from this bin will capture information on: UT-047009 Bin 17 Average minor allele frequency of sites in this bin: 19 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-032637 A TagSNP from this bin will capture information on: UI-032637 Bin 18 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-005178 A TagSNP from this bin will capture information on: UI-005178 Bin 19 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047721 A TagSNP from this bin will capture information on: UT-047721 Bin 20 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-044663 A TagSNP from this bin will capture information on: UI-044663 Bin 21 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-033824 A TagSNP from this bin will capture information on: UI-033824 Bin 22 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-021718 A TagSNP from this bin will capture information on: UI-021718 Bin 23 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-034053 A TagSNP from this bin will capture information on: UI-034053 Bin 24 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-000747 A TagSNP from this bin will capture information on: UF-000747 Bin 25 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UN-046573 A TagSNP from this bin will capture information on: UN-046573 Bin 26 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-014432 A TagSNP from this bin will capture information on: UI-014432 Bin 27 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-037649 A TagSNP from this bin will capture information on: RI-037649 Bin 28 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-031673 A TagSNP from this bin will capture information on: UI-031673 Bin 29 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-029249 A TagSNP from this bin will capture information on: UI-029249 Bin 30 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-012125 A TagSNP from this bin will capture information on: UI-012125 Bin 31 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-006932 A TagSNP from this bin will capture information on: RI-006932 Bin 32 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-006492 A TagSNP from this bin will capture information on: UI-006492 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-047822 A TagSNP from this bin will capture information on: UF-047822 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047479 A TagSNP from this bin will capture information on: UT-047479 Bin 35 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047407 A TagSNP from this bin will capture information on: UT-047407 Bin 36 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047384 A TagSNP from this bin will capture information on: UT-047384 Bin 37 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047240 A TagSNP from this bin will capture information on: UT-047240 Bin 38 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047058 A TagSNP from this bin will capture information on: UT-047058 Bin 39 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047005 A TagSNP from this bin will capture information on: UT-047005 Bin 40 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-046993 A TagSNP from this bin will capture information on: UT-046993 Bin 41 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-046925 A TagSNP from this bin will capture information on: UT-046925 Bin 42 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1