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% 153 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 92 bins found. Bin 1 Average minor allele frequency of sites in this bin: 23 % # SNPs in this bin: 57 Assay one of these TagSNPs: UF-000074 RF-000217 RF-000306 UF-000634 UF-000892 US-001185 UI-002213 UI-002318 UI-002419 UI-002733 UI-019223 UI-019329 RI-019403 A TagSNP from this bin will capture information on: UF-000074 RF-000217 RF-000306 UF-000634 UF-000892 US-001185 UI-002213 UI-002318 UI-002419 UI-002733 RI-003111 RI-003115 RI-003157 RI-003200 UI-003476 UI-003852 UI-004161 RI-004208 RI-004545 RI-004546 RI-004636 RI-004641 RI-004653 UI-004752 UI-004810 RI-005190 UI-005346 UI-005435 RI-005657 UI-005809 UI-006370 RI-007366 RI-007391 RI-007575 UI-007846 RI-009922 RI-009923 RI-010021 UI-010472 UI-011015 UI-011066 RI-011395 UI-011583 RI-013324 RI-013356 UI-014769 UI-014903 UI-014974 UI-015362 UI-015664 UI-015670 UI-015696 RI-018753 RI-018793 UI-019223 UI-019329 RI-019403 Bin 2 Average minor allele frequency of sites in this bin: 38 % # SNPs in this bin: 23 Assay one of these TagSNPs: RI-011265 A TagSNP from this bin will capture information on: US-006054 RI-006729 RI-007064 RI-007828 UI-008021 RI-008111 RI-008130 RI-008356 RI-008519 RI-008559 UI-008645 UN-008830 RI-011265 RI-016541 UI-016838 RI-017521 UI-019255 UI-020518 RI-021165 RI-021884 RI-022126 RI-022373 UI-024662 Bin 3 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 10 Assay one of these TagSNPs: RI-017167 UI-019062 UI-026115 UI-026450 UI-026562 UI-027498 A TagSNP from this bin will capture information on: RI-017137 RI-017167 UI-019062 RI-020915 UI-025815 UI-025986 UI-026115 UI-026450 UI-026562 UI-027498 Bin 4 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-006294 RI-007635 RI-016675 UI-017016 RI-018842 UI-019158 A TagSNP from this bin will capture information on: UI-006294 RI-007635 RI-016675 UI-017016 RI-018842 UI-019158 Bin 5 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 6 Assay one of these TagSNPs: UF-000702 US-003759 RI-005112 UI-014708 UI-022547 UI-023672 A TagSNP from this bin will capture information on: UF-000702 US-003759 RI-005112 UI-014708 UI-022547 UI-023672 Bin 6 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-004129 UI-011180 UI-014978 UI-020632 UI-022012 A TagSNP from this bin will capture information on: UI-004129 UI-011180 UI-014978 UI-020632 UI-022012 Bin 7 Average minor allele frequency of sites in this bin: 32 % # SNPs in this bin: 5 Assay one of these TagSNPs: RI-012876 A TagSNP from this bin will capture information on: RI-004465 RI-004489 RI-012876 UI-015849 UI-027217 Bin 8 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-025250 RI-025289 UI-025567 UI-026267 A TagSNP from this bin will capture information on: RI-025250 RI-025289 UI-025567 UI-026267 Bin 9 Average minor allele frequency of sites in this bin: 32 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-014376 A TagSNP from this bin will capture information on: RI-014253 UI-014376 RI-018828 UI-019054 Bin 10 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-014611 RI-017271 UF-028496 A TagSNP from this bin will capture information on: UI-014611 RI-017271 UF-028496 Bin 11 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-004369 RI-005540 A TagSNP from this bin will capture information on: UI-004369 RI-005540 Bin 12 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-006798 RI-006840 A TagSNP from this bin will capture information on: RI-006798 RI-006840 Bin 13 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-004297 RI-021907 A TagSNP from this bin will capture information on: RI-004297 RI-021907 Bin 14 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-005958 UI-015047 A TagSNP from this bin will capture information on: UI-005958 UI-015047 Bin 15 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-008942 RI-020030 A TagSNP from this bin will capture information on: UI-008942 RI-020030 Bin 16 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-014902 RI-016643 A TagSNP from this bin will capture information on: UI-014902 RI-016643 Bin 17 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-008424 RI-008517 A TagSNP from this bin will capture information on: RI-008424 RI-008517 Bin 18 Average minor allele frequency of sites in this bin: 23 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-027521 UI-027556 A TagSNP from this bin will capture information on: UI-027521 UI-027556 Bin 19 Average minor allele frequency of sites in this bin: 15 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-021816 UI-027431 A TagSNP from this bin will capture information on: RI-021816 UI-027431 Bin 20 Average minor allele frequency of sites in this bin: 39 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-028672 A TagSNP from this bin will capture information on: RF-028672 Bin 21 Average minor allele frequency of sites in this bin: 30 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-029183 A TagSNP from this bin will capture information on: UF-029183 Bin 22 Average minor allele frequency of sites in this bin: 25 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004685 A TagSNP from this bin will capture information on: RI-004685 Bin 23 Average minor allele frequency of sites in this bin: 23 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013989 A TagSNP from this bin will capture information on: UI-013989 Bin 24 Average minor allele frequency of sites in this bin: 21 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-004990 A TagSNP from this bin will capture information on: UI-004990 Bin 25 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-016686 A TagSNP from this bin will capture information on: RI-016686 Bin 26 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027689 A TagSNP from this bin will capture information on: UI-027689 Bin 27 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-011916 A TagSNP from this bin will capture information on: UI-011916 Bin 28 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-024183 A TagSNP from this bin will capture information on: RI-024183 Bin 29 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-025523 A TagSNP from this bin will capture information on: UI-025523 Bin 30 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-012823 A TagSNP from this bin will capture information on: RI-012823 Bin 31 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004586 A TagSNP from this bin will capture information on: RI-004586 Bin 32 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-028968 A TagSNP from this bin will capture information on: RF-028968 Bin 33 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-028873 A TagSNP from this bin will capture information on: RF-028873 Bin 34 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-028042 A TagSNP from this bin will capture information on: UT-028042 Bin 35 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027315 A TagSNP from this bin will capture information on: UI-027315 Bin 36 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-026734 A TagSNP from this bin will capture information on: UI-026734 Bin 37 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-026725 A TagSNP from this bin will capture information on: UI-026725 Bin 38 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-026568 A TagSNP from this bin will capture information on: UI-026568 Bin 39 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-024979 A TagSNP from this bin will capture information on: UI-024979 Bin 40 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-024120 A TagSNP from this bin will capture information on: RI-024120 Bin 41 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-023960 A TagSNP from this bin will capture information on: RI-023960 Bin 42 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-023567 A TagSNP from this bin will capture information on: UI-023567 Bin 43 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-023094 A TagSNP from this bin will capture information on: UI-023094 Bin 44 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021845 A TagSNP from this bin will capture information on: RI-021845 Bin 45 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021702 A TagSNP from this bin will capture information on: RI-021702 Bin 46 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-021468 A TagSNP from this bin will capture information on: UI-021468 Bin 47 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-021457 A TagSNP from this bin will capture information on: UI-021457 Bin 48 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-020993 A TagSNP from this bin will capture information on: RI-020993 Bin 49 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-020978 A TagSNP from this bin will capture information on: RI-020978 Bin 50 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-020785 A TagSNP from this bin will capture information on: UI-020785 Bin 51 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-020275 A TagSNP from this bin will capture information on: UI-020275 Bin 52 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-020053 A TagSNP from this bin will capture information on: RI-020053 Bin 53 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-018001 A TagSNP from this bin will capture information on: RI-018001 Bin 54 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017492 A TagSNP from this bin will capture information on: RI-017492 Bin 55 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017491 A TagSNP from this bin will capture information on: RI-017491 Bin 56 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017281 A TagSNP from this bin will capture information on: RI-017281 Bin 57 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-017255 A TagSNP from this bin will capture information on: UI-017255 Bin 58 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017237 A TagSNP from this bin will capture information on: RI-017237 Bin 59 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-016975 A TagSNP from this bin will capture information on: UI-016975 Bin 60 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-016585 A TagSNP from this bin will capture information on: RI-016585 Bin 61 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-015969 A TagSNP from this bin will capture information on: UI-015969 Bin 62 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-014527 A TagSNP from this bin will capture information on: UI-014527 Bin 63 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013660 A TagSNP from this bin will capture information on: UI-013660 Bin 64 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-013417 A TagSNP from this bin will capture information on: RI-013417 Bin 65 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-013385 A TagSNP from this bin will capture information on: RI-013385 Bin 66 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-013348 A TagSNP from this bin will capture information on: RI-013348 Bin 67 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-012572 A TagSNP from this bin will capture information on: RI-012572 Bin 68 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-012415 A TagSNP from this bin will capture information on: RI-012415 Bin 69 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-012058 A TagSNP from this bin will capture information on: RI-012058 Bin 70 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-011814 A TagSNP from this bin will capture information on: UI-011814 Bin 71 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1