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% 253 sites exceeding this frequency threshold were found. r^2 threshold for LDselect 0.64 96 bins found. Bin 1 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 31 Assay one of these TagSNPs: RI-027133 UI-032321 UI-036353 UI-036635 UI-037040 RI-037795 RI-037933 UI-038259 UI-038369 UI-038749 UI-039572 UI-039605 UI-039615 UI-039650 UI-039731 UI-039922 UI-040040 UI-040140 UI-041111 RI-041499 UI-041575 UI-041608 UI-041696 UI-042040 A TagSNP from this bin will capture information on: RF-000311 UI-004864 UI-007682 UI-007880 RI-027133 UI-032321 UI-036353 UI-036635 UI-037040 RI-037795 RI-037933 UI-038259 UI-038369 UI-038749 UI-039572 UI-039605 UI-039615 UI-039650 UI-039731 UI-039922 UI-040040 UI-040140 UI-041111 RI-041499 UI-041575 UI-041608 UI-041696 UI-042040 UI-044663 UI-045206 UT-046925 Bin 2 Average minor allele frequency of sites in this bin: 30 % # SNPs in this bin: 13 Assay one of these TagSNPs: UI-043316 UI-043452 RI-043737 RI-043919 UI-044494 UI-044866 UI-044931 UI-045145 UI-045181 UI-045271 UI-045279 UI-045312 UI-045484 A TagSNP from this bin will capture information on: UI-043316 UI-043452 RI-043737 RI-043919 UI-044494 UI-044866 UI-044931 UI-045145 UI-045181 UI-045271 UI-045279 UI-045312 UI-045484 Bin 3 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 13 Assay one of these TagSNPs: UI-008263 RI-008897 UI-010243 UI-011161 RI-011974 UI-013005 UI-013489 UI-013578 UI-013973 UI-014051 UI-014148 UI-014359 UI-017272 A TagSNP from this bin will capture information on: UI-008263 RI-008897 UI-010243 UI-011161 RI-011974 UI-013005 UI-013489 UI-013578 UI-013973 UI-014051 UI-014148 UI-014359 UI-017272 Bin 4 Average minor allele frequency of sites in this bin: 34 % # SNPs in this bin: 12 Assay one of these TagSNPs: UI-018142 RI-019050 RI-019070 RI-019262 UI-019487 UI-019750 UI-020018 UI-020371 A TagSNP from this bin will capture information on: UI-018142 RI-019050 RI-019070 RI-019262 UI-019387 UI-019487 UI-019610 UI-019750 UI-020018 UI-020371 UI-021705 UI-021936 Bin 5 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 11 Assay one of these TagSNPs: UI-028604 UI-032203 UI-032926 UF-047822 A TagSNP from this bin will capture information on: UI-003336 RI-019231 UI-021415 UI-027394 UI-028604 RI-028997 UI-029974 RI-030480 UI-032203 UI-032926 UF-047822 Bin 6 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 10 Assay one of these TagSNPs: UI-003529 UI-004205 UI-012109 UI-014679 UI-015373 UI-017785 UI-019982 UI-023327 RI-024522 UI-025158 A TagSNP from this bin will capture information on: UI-003529 UI-004205 UI-012109 UI-014679 UI-015373 UI-017785 UI-019982 UI-023327 RI-024522 UI-025158 Bin 7 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-012919 UI-014183 UI-018281 UI-019658 UI-022372 UI-023636 UI-043038 UN-046330 A TagSNP from this bin will capture information on: UI-012919 UI-014183 UI-018281 UI-019658 UI-022372 UI-023636 UI-043038 UN-046330 Bin 8 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-007639 UI-008726 UI-009309 UI-010711 RI-014748 RI-014828 RI-015743 UI-032012 A TagSNP from this bin will capture information on: UI-007639 UI-008726 UI-009309 UI-010711 RI-014748 RI-014828 RI-015743 UI-032012 Bin 9 Average minor allele frequency of sites in this bin: 5 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-004601 UI-005327 RI-006893 RI-006894 RI-006999 RI-007060 UI-007271 UI-040294 A TagSNP from this bin will capture information on: UI-004601 UI-005327 RI-006893 RI-006894 RI-006999 RI-007060 UI-007271 UI-040294 Bin 10 Average minor allele frequency of sites in this bin: 38 % # SNPs in this bin: 8 Assay one of these TagSNPs: UI-025525 RI-026623 RI-026808 UI-028640 A TagSNP from this bin will capture information on: UI-024446 RI-024552 UI-024708 UI-025525 RI-026623 RI-026808 UI-028640 UI-030288 Bin 11 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 7 Assay one of these TagSNPs: RI-006839 UI-007720 UI-024646 UI-034351 UI-040911 UI-042993 UT-047005 A TagSNP from this bin will capture information on: RI-006839 UI-007720 UI-024646 UI-034351 UI-040911 UI-042993 UT-047005 Bin 12 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 6 Assay one of these TagSNPs: RF-000102 UI-004956 UI-007810 UI-008544 UI-036789 UI-039190 A TagSNP from this bin will capture information on: RF-000102 UI-004956 UI-007810 UI-008544 UI-036789 UI-039190 Bin 13 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-004671 UI-005391 UI-006517 UI-020075 RI-030478 UI-041200 A TagSNP from this bin will capture information on: UI-004671 UI-005391 UI-006517 UI-020075 RI-030478 UI-041200 Bin 14 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 6 Assay one of these TagSNPs: UI-018635 UI-021076 UI-021651 UI-034456 UI-037202 UI-041256 A TagSNP from this bin will capture information on: UI-018635 UI-021076 UI-021651 UI-034456 UI-037202 UI-041256 Bin 15 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 5 Assay one of these TagSNPs: RF-000094 RF-000095 RF-001521 UI-007789 UI-043683 A TagSNP from this bin will capture information on: RF-000094 RF-000095 RF-001521 UI-007789 UI-043683 Bin 16 Average minor allele frequency of sites in this bin: 35 % # SNPs in this bin: 5 Assay one of these TagSNPs: RF-001896 A TagSNP from this bin will capture information on: RF-000478 RF-001896 RF-001993 UI-004052 UI-006203 Bin 17 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-004697 RI-009039 UI-013408 UI-017312 A TagSNP from this bin will capture information on: UI-004697 RI-009039 UI-013408 UI-017312 Bin 18 Average minor allele frequency of sites in this bin: 11 % # SNPs in this bin: 4 Assay one of these TagSNPs: RF-002186 UI-009205 RI-015687 UI-022772 A TagSNP from this bin will capture information on: RF-002186 UI-009205 RI-015687 UI-022772 Bin 19 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 4 Assay one of these TagSNPs: UI-035440 A TagSNP from this bin will capture information on: UI-035440 RI-037609 UI-042069 UI-043481 Bin 20 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-013632 UI-020830 UI-021718 A TagSNP from this bin will capture information on: UI-013632 UI-020830 UI-021718 Bin 21 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: RF-000150 UI-013733 UI-032539 A TagSNP from this bin will capture information on: RF-000150 UI-013733 UI-032539 Bin 22 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-033483 RI-043757 UI-045031 A TagSNP from this bin will capture information on: UI-033483 RI-043757 UI-045031 Bin 23 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 3 Assay one of these TagSNPs: RF-000446 UI-003679 UI-003729 A TagSNP from this bin will capture information on: RF-000446 UI-003679 UI-003729 Bin 24 Average minor allele frequency of sites in this bin: 32 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-033401 UI-034778 UI-040348 A TagSNP from this bin will capture information on: UI-033401 UI-034778 UI-040348 Bin 25 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 3 Assay one of these TagSNPs: RI-027002 UI-029567 UT-047407 A TagSNP from this bin will capture information on: RI-027002 UI-029567 UT-047407 Bin 26 Average minor allele frequency of sites in this bin: 13 % # SNPs in this bin: 3 Assay one of these TagSNPs: UT-047240 A TagSNP from this bin will capture information on: RI-037618 UI-042956 UT-047240 Bin 27 Average minor allele frequency of sites in this bin: 30 % # SNPs in this bin: 3 Assay one of these TagSNPs: UI-013802 A TagSNP from this bin will capture information on: RI-004381 UI-013802 UI-022531 Bin 28 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-004743 UI-004755 A TagSNP from this bin will capture information on: UI-004743 UI-004755 Bin 29 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-010095 RI-011668 A TagSNP from this bin will capture information on: UI-010095 RI-011668 Bin 30 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-012890 UI-017146 A TagSNP from this bin will capture information on: UI-012890 UI-017146 Bin 31 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-039904 UI-040903 A TagSNP from this bin will capture information on: UI-039904 UI-040903 Bin 32 Average minor allele frequency of sites in this bin: 23 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-042810 UI-042866 A TagSNP from this bin will capture information on: UI-042810 UI-042866 Bin 33 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-043649 UI-044904 A TagSNP from this bin will capture information on: UI-043649 UI-044904 Bin 34 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-021120 UI-021764 A TagSNP from this bin will capture information on: UI-021120 UI-021764 Bin 35 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-004739 UI-038214 A TagSNP from this bin will capture information on: UI-004739 UI-038214 Bin 36 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 2 Assay one of these TagSNPs: RI-016782 UI-021426 A TagSNP from this bin will capture information on: RI-016782 UI-021426 Bin 37 Average minor allele frequency of sites in this bin: 45 % # 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 38 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-010005 RI-016710 A TagSNP from this bin will capture information on: UI-010005 RI-016710 Bin 39 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 2 Assay one of these TagSNPs: UI-027666 UT-047384 A TagSNP from this bin will capture information on: UI-027666 UT-047384 Bin 40 Average minor allele frequency of sites in this bin: 47 % # SNPs in this bin: 1 Assay one of these TagSNPs: UF-001568 A TagSNP from this bin will capture information on: UF-001568 Bin 41 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-042559 A TagSNP from this bin will capture information on: UI-042559 Bin 42 Average minor allele frequency of sites in this bin: 45 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-009185 A TagSNP from this bin will capture information on: RI-009185 Bin 43 Average minor allele frequency of sites in this bin: 43 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-023476 A TagSNP from this bin will capture information on: UI-023476 Bin 44 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-031747 A TagSNP from this bin will capture information on: UI-031747 Bin 45 Average minor allele frequency of sites in this bin: 41 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-023225 A TagSNP from this bin will capture information on: UI-023225 Bin 46 Average minor allele frequency of sites in this bin: 33 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-007526 A TagSNP from this bin will capture information on: UI-007526 Bin 47 Average minor allele frequency of sites in this bin: 31 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047721 A TagSNP from this bin will capture information on: UT-047721 Bin 48 Average minor allele frequency of sites in this bin: 27 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-046905 A TagSNP from this bin will capture information on: US-046905 Bin 49 Average minor allele frequency of sites in this bin: 26 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-032637 A TagSNP from this bin will capture information on: UI-032637 Bin 50 Average minor allele frequency of sites in this bin: 25 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-008266 A TagSNP from this bin will capture information on: UI-008266 Bin 51 Average minor allele frequency of sites in this bin: 23 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-019592 A TagSNP from this bin will capture information on: UI-019592 Bin 52 Average minor allele frequency of sites in this bin: 17 % # SNPs in this bin: 1 Assay one of these TagSNPs: US-046416 A TagSNP from this bin will capture information on: US-046416 Bin 53 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047360 A TagSNP from this bin will capture information on: UT-047360 Bin 54 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-023673 A TagSNP from this bin will capture information on: UI-023673 Bin 55 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-005925 A TagSNP from this bin will capture information on: UI-005925 Bin 56 Average minor allele frequency of sites in this bin: 14 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-003603 A TagSNP from this bin will capture information on: UI-003603 Bin 57 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-016749 A TagSNP from this bin will capture information on: RI-016749 Bin 58 Average minor allele frequency of sites in this bin: 12 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-007302 A TagSNP from this bin will capture information on: UI-007302 Bin 59 Average minor allele frequency of sites in this bin: 10 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-046993 A TagSNP from this bin will capture information on: UT-046993 Bin 60 Average minor allele frequency of sites in this bin: 8 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-029660 A TagSNP from this bin will capture information on: UI-029660 Bin 61 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-009997 A TagSNP from this bin will capture information on: UI-009997 Bin 62 Average minor allele frequency of sites in this bin: 6 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-001778 A TagSNP from this bin will capture information on: RF-001778 Bin 63 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047058 A TagSNP from this bin will capture information on: UT-047058 Bin 64 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-034635 A TagSNP from this bin will capture information on: UI-034635 Bin 65 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013214 A TagSNP from this bin will capture information on: UI-013214 Bin 66 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-012125 A TagSNP from this bin will capture information on: UI-012125 Bin 67 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-008958 A TagSNP from this bin will capture information on: RI-008958 Bin 68 Average minor allele frequency of sites in this bin: 4 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-006607 A TagSNP from this bin will capture information on: UI-006607 Bin 69 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047479 A TagSNP from this bin will capture information on: UT-047479 Bin 70 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RI-037839 A TagSNP from this bin will capture information on: RI-037839 Bin 71 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-019738 A TagSNP from this bin will capture information on: UI-019738 Bin 72 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-013590 A TagSNP from this bin will capture information on: UI-013590 Bin 73 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: UI-005178 A TagSNP from this bin will capture information on: UI-005178 Bin 74 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-001224 A TagSNP from this bin will capture information on: RF-001224 Bin 75 Average minor allele frequency of sites in this bin: 2 % # SNPs in this bin: 1 Assay one of these TagSNPs: RF-000134 A TagSNP from this bin will capture information on: RF-000134 Bin 76 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1 Assay one of these TagSNPs: UT-047009 A TagSNP from this bin will capture information on: UT-047009 Bin 77 Average minor allele frequency of sites in this bin: 0 % # SNPs in this bin: 1