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% 197 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 76 bins found. Bin 1 Average minor allele frequency of sites in this bin: 40 % # SNPs in this bin: 31 Assay one of these TagSNPs: RI-012876 A TagSNP from this bin will capture information on: UI-004161 RI-004208 RI-004465 RI-004546 RI-004641 UI-004752 UI-004810 RI-005190 UI-005346 UI-005435 RI-005657 UI-005809 RI-012876 RI-013324 RI-013356 RI-014253 UI-014376 UI-014769 UI-014903 UI-014974 UI-015362 UI-015664 UI-015670 UI-015696 UI-015849 RI-018753 RI-018793 RI-018828 UI-019054 UI-019223 RI-019403 Bin 2 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 17 Assay one of these TagSNPs: RI-003111 RI-003115 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-003200 UI-003476 RI-004489 RI-004545 UI-004990 Bin 3 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 12 Assay one of these TagSNPs: UI-003852 RI-004636 UI-006370 RI-007575 UI-007846 RI-009922 RI-009923 RI-010021 UI-010472 UI-011015 UI-011066 UI-013989 A TagSNP from this bin will capture information on: UI-003852 RI-004636 UI-006370 RI-007575 UI-007846 RI-009922 RI-009923 RI-010021 UI-010472 UI-011015 UI-011066 UI-013989 Bin 4 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 11 Assay one of these TagSNPs: RI-007828 UI-008021 RI-008111 RI-008130 RI-008424 RI-008519 RI-008559 UI-008645 UN-008830 A TagSNP from this bin will capture information on: RI-007064 RI-007828 UI-008021 RI-008111 RI-008130 RI-008424 RI-008517 RI-008519 RI-008559 UI-008645 UN-008830 Bin 5 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 8 Assay one of these TagSNPs: RF-000323 UF-001016 RI-005606 UI-006417 RI-009996 RI-010185 UI-011814 RI-012058 A TagSNP from this bin will capture information on: RF-000323 UF-001016 RI-005606 UI-006417 RI-009996 RI-010185 UI-011814 RI-012058 Bin 6 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 8 Assay one of these TagSNPs: RI-003192 UI-005909 RI-006887 UI-007974 RI-009933 UI-010264 RI-013417 UI-014527 A TagSNP from this bin will capture information on: RI-003192 UI-005909 RI-006887 UI-007974 RI-009933 UI-010264 RI-013417 UI-014527 Bin 7 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 7 Assay one of these TagSNPs: RI-016585 RI-018001 UI-026734 A TagSNP from this bin will capture information on: UI-004143 RI-012415 RI-016585 RI-018001 RI-020978 RI-020993 UI-026734 Bin 8 Average minor allele frequency of sites in this bin: 44 % # SNPs in this bin: 6 Assay one of these TagSNPs: RI-025250 A TagSNP from this bin will capture information on: RI-021884 RI-022126 RI-025250 RI-025289 UI-025567 UI-026267 Bin 9 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-025523 UI-025815 UI-025986 UI-026115 UI-026450 UI-026562 A TagSNP from this bin will capture information on: UI-025523 UI-025815 UI-025986 UI-026115 UI-026450 UI-026562 Bin 10 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 5 Assay one of these TagSNPs: UF-000702 RI-008263 RI-017492 RI-021702 UI-023094 A TagSNP from this bin will capture information on: UF-000702 RI-008263 RI-017492 RI-021702 UI-023094 Bin 11 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 5 Assay one of these TagSNPs: UI-016975 UI-020275 UI-023567 RI-024120 UI-026725 A TagSNP from this bin will capture information on: UI-016975 UI-020275 UI-023567 RI-024120 UI-026725 Bin 12 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-004350 RI-007416 UN-010924 RI-013385 A TagSNP from this bin will capture information on: UI-004350 RI-007416 UN-010924 RI-013385 Bin 13 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 4 Assay one of these TagSNPs: UN-008784 RI-013348 RI-017237 RF-028968 A TagSNP from this bin will capture information on: UN-008784 RI-013348 RI-017237 RF-028968 Bin 14 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 4 Assay one of these TagSNPs: RI-007366 RI-007391 RI-011395 UI-011583 A TagSNP from this bin will capture information on: RI-007366 RI-007391 RI-011395 UI-011583 Bin 15 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-005775 A TagSNP from this bin will capture information on: UF-000612 UI-004129 UI-005775 UI-020785 Bin 16 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-024662 A TagSNP from this bin will capture information on: US-006054 RI-017521 UI-019255 UI-024662 Bin 17 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: US-003759 RI-005112 UI-005352 A TagSNP from this bin will capture information on: US-003759 RI-005112 UI-005352 Bin 18 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-005704 UI-027498 UT-028042 A TagSNP from this bin will capture information on: RI-005704 UI-027498 UT-028042 Bin 19 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-015969 UI-021468 UI-024979 A TagSNP from this bin will capture information on: UI-015969 UI-021468 UI-024979 Bin 20 Average minor allele frequency of sites in this bin: 28 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-020518 RI-021165 RI-022373 A TagSNP from this bin will capture information on: UI-020518 RI-021165 RI-022373 Bin 21 Average minor allele frequency of sites in this bin: 41 % # 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 22 Average minor allele frequency of sites in this bin: 31 % # 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 23 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-006294 RI-007635 A TagSNP from this bin will capture information on: UI-006294 RI-007635 Bin 24 Average minor allele frequency of sites in this bin: 8 % # 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 25 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-018842 UI-019158 A TagSNP from this bin will capture information on: RI-018842 UI-019158 Bin 26 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-017491 RI-023960 A TagSNP from this bin will capture information on: RI-017491 RI-023960 Bin 27 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-014978 UI-020632 A TagSNP from this bin will capture information on: UI-014978 UI-020632 Bin 28 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-020053 UI-021457 A TagSNP from this bin will capture information on: RI-020053 UI-021457 Bin 29 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-016675 UI-017016 A TagSNP from this bin will capture information on: RI-016675 UI-017016 Bin 30 Average minor allele frequency of sites in this bin: 9 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-014611 RI-020915 A TagSNP from this bin will capture information on: UI-014611 RI-020915 Bin 31 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027556 A TagSNP from this bin will capture information on: UI-027556 Bin 32 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004653 A TagSNP from this bin will capture information on: RI-004653 Bin 33 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027217 A TagSNP from this bin will capture information on: UI-027217 Bin 34 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-016541 A TagSNP from this bin will capture information on: RI-016541 Bin 35 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-016838 A TagSNP from this bin will capture information on: UI-016838 Bin 36 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004685 A TagSNP from this bin will capture information on: RI-004685 Bin 37 Average minor allele frequency of sites in this bin: 37 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-028672 A TagSNP from this bin will capture information on: RF-028672 Bin 38 Average minor allele frequency of sites in this bin: 36 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-003157 A TagSNP from this bin will capture information on: RI-003157 Bin 39 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-011265 A TagSNP from this bin will capture information on: RI-011265 Bin 40 Average minor allele frequency of sites in this bin: 33 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-006729 A TagSNP from this bin will capture information on: RI-006729 Bin 41 Average minor allele frequency of sites in this bin: 29 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027431 A TagSNP from this bin will capture information on: UI-027431 Bin 42 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-029183 A TagSNP from this bin will capture information on: UF-029183 Bin 43 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-008356 A TagSNP from this bin will capture information on: RI-008356 Bin 44 Average minor allele frequency of sites in this bin: 25 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-019329 A TagSNP from this bin will capture information on: UI-019329 Bin 45 Average minor allele frequency of sites in this bin: 20 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-028496 A TagSNP from this bin will capture information on: UF-028496 Bin 46 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027521 A TagSNP from this bin will capture information on: UI-027521 Bin 47 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-028873 A TagSNP from this bin will capture information on: RF-028873 Bin 48 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-026568 A TagSNP from this bin will capture information on: UI-026568 Bin 49 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027689 A TagSNP from this bin will capture information on: UI-027689 Bin 50 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013660 A TagSNP from this bin will capture information on: UI-013660 Bin 51 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-012572 A TagSNP from this bin will capture information on: RI-012572 Bin 52 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-027315 A TagSNP from this bin will capture information on: UI-027315 Bin 53 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-017255 A TagSNP from this bin will capture information on: UI-017255 Bin 54 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 55 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021845 A TagSNP from this bin will capture information on: RI-021845 Bin 56 Average minor allele frequency of sites in this bin: 2 % # 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: 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 58 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-011180 A TagSNP from this bin will capture information on: UI-011180 Bin 59 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 60 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-023672 A TagSNP from this bin will capture information on: UI-023672 Bin 61 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-022547 A TagSNP from this bin will capture information on: UI-022547 Bin 62 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-022012 A TagSNP from this bin will capture information on: UI-022012 Bin 63 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021907 A TagSNP from this bin will capture information on: RI-021907 Bin 64 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-021816 A TagSNP from this bin will capture information on: RI-021816 Bin 65 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-020030 A TagSNP from this bin will capture information on: RI-020030 Bin 66 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-019062 A TagSNP from this bin will capture information on: UI-019062 Bin 67 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017271 A TagSNP from this bin will capture information on: RI-017271 Bin 68 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017167 A TagSNP from this bin will capture information on: RI-017167 Bin 69 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-017137 A TagSNP from this bin will capture information on: RI-017137 Bin 70 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-016686 A TagSNP from this bin will capture information on: RI-016686 Bin 71 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-015047 A TagSNP from this bin will capture information on: UI-015047 Bin 72 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-014708 A TagSNP from this bin will capture information on: UI-014708 Bin 73 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-011916 A TagSNP from this bin will capture information on: UI-011916 Bin 74 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-008942 A TagSNP from this bin will capture information on: UI-008942 Bin 75 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-005958 A TagSNP from this bin will capture information on: UI-005958 Bin 76 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-004297 A TagSNP from this bin will capture information on: RI-004297