Table 5 List of SNPs assigned a different chromosome by LODE as compared to Btau4.0 and 5 problem regions in Btau4.0 identified by LODE.
Btau4.0 | LODE | UMD3.0 | ||||
|---|---|---|---|---|---|---|
SNP Assay ID | Chrom osome | Position (bp) | Chrom osome | Position (bp) | Chromosome: Position (bp) | Problem region |
ARS-BFGL-NGS-26766 | 1 | 114010038 | 2 | 69089678 | 2:71023597 | |
1861431 | 1 | 144225095 | 15 | 47262164 | 1:142952903 | |
BTA-45006-no-rs | 2 | 10760381 | 4 | 34049395 | 4:33987224 | |
1876171 | 2 | 56762771 | 10 | 43036781 | 2:54560749 | |
1873289 | 2 | 94496897 | 11 | 59283090 | 11:61135811 | |
ARS-BFGL-NGS-32344 | 3 | 30329145 | 11 | 36536145 | 3:27963904 | |
ARS-BFGL-NGS-115797 | 3 | 77488731 | 2 | 126296914 | 2:118277989 | 1 |
343487 | 3 | 77719948 | 2 | 125113698 | 2:118048961 | 1 |
351668 | 3 | 77757827 | 2 | 120653554 | 2:118011142 | 1 |
ARS-BFGL-NGS-89183 | 3 | 77786834 | 2 | 125153297 | 2:117982134 | 1 |
ARS-BFGL-NGS-317 | 3 | 77822712 | 2 | 123366377 | 2:117946210 | 1 |
1871424 | 3 | 77859105 | 2 | 121859331 | 2:117909817 | 1 |
ARS-BFGL-NGS-70541 | 3 | 127719186 | 22 | 60528302 | 22:60785491 | 2 |
1870128 | 3 | 127750012 | 22 | 57739278 | 22:60755275 | 2 |
ARS-BFGL-NGS-58676 | 3 | 127769201 | 22 | 61298196 | 22:60736089 | 2 |
ARS-BFGL-NGS-2807 | 3 | 127874807 | 22 | 54335047 | 22:60634400 | 2 |
ARS-BFGL-NGS-19124 | 3 | 127908628 | 22 | 61358781 | 22:60600490 | 2 |
ARS-BFGL-NGS-8807 | 4 | 2607777 | 11 | 40976163 | 4:2676685 | |
ARS-BFGL-NGS-113798 | 4 | 4445195 | 10 | 30252857 | 4:4340312 | |
ARS-BFGL-NGS-15424 | 4 | 83768798 | 14 | 78612579 | 14:81878266 | |
344491 | 4 | 110028200 | 23 | 28037374 | 4:106890553//8:91314567 | |
1867566 | 5 | 5331062 | 1 | 120905947 | 5:5049476 | |
1868001 | 5 | 94598147 | 14 | 11525489 | 5:88617706 | |
BTA-110801-no-rs | 5 | 96742247 | 1 | 16408220 | 1:16094228 | |
BTA-74608-no-rs | 5 | 102914139 | 10 | 66434699 | 5:96344375 | |
464972 | 6 | 36820192 | 9 | 49534891 | 6:37434546 | |
Hapmap38285-BTA-110077 | 7 | 25557308 | 19 | 51160026 | 7:27891275 | |
1867647 | 7 | 60836776 | 18 | 6943970 | 7:63367359 | |
BTB-00316147 | 7 | 62064599 | 17 | 13362033 | 17:12137554 | |
BTA-98858-no-rs | 7 | 77340598 | X | 69412698 | X:121600055 | |
1873146 | 8 | 7400266 | 16 | 38314751 | 8:7357495 | |
464622 | 8 | 70460363 | 18 | 26000936 | 11:9122777 //18:24282247 //8:67661725 | |
BTA-97336-no-rs | 9 | 3823907 | 1 | 125108946 | 9:4581947 | |
1865493 | 9 | 54935966 | 11 | 22728050 | 9:53194372 | |
BTB-01806856 | 9 | 81376121 | 1 | 61983636 | 1:62607089 | |
1866405 | 9 | 103328739 | 13 | 68455077 | 9:100810058 | |
ARS-BFGL-NGS-92893 | 10 | 3905779 | 2 | 110967662 | 10:4340696 | |
ARS-BFGL-NGS-73149 | 10 | 15513722 | 1 | 35290138 | 1:30259943 | 3 |
BTA-97531-no-rs | 10 | 15578191 | 1 | 32951433 | 1:30333360 | 3 |
BTB-01490270 | 10 | 15659183 | 1 | 31342947 | 1:30414871 | 3 |
1874946 | 10 | 17857141 | 11 | 18153873 | 10:17528963 | |
BTA-88378-no-rs | 10 | 62466743 | 4 | 71372575 | 4:71413010 | 4 |
Hapmap28362-BTA-48086 | 10 | 62487185 | 4 | 68238697 | 4:71433452 | 4 |
ARS-BFGL-NGS-53167 | 10 | 62712521 | 4 | 69590750 | 4:71603530 | 4 |
BTA-109199-no-rs | 10 | 62734149 | 4 | 71457638 | 4:71625158 | 4 |
1875511 | 10 | 62741080 | 4 | 72626961 | 4:71632089 | 4 |
ARS-BFGL-BAC-6642 | 11 | 7361519 | 4 | 37715495 | 4:37109034 | 4 |
1861989 | 11 | 98919723 | 2 | 90294746 | 11:95497623 | |
ARS-BFGL-BAC-5532 | 12 | 14460102 | 25 | 1759284 | 12:15518882 //25:1416859 | |
349300 | 12 | 41051742 | 11 | 64226960 | 11:65590436 | |
1874001 | 12 | 69506929 | 8 | 47841259 | 12:72414147 | |
BTB-01588251 | 13 | 3055670 | 18 | 45334043 | 18:45474850 | |
344445 | 13 | 65183788 | 4 | 85581292 | 13:65259657 | |
464345 | 13 | 82520352 | 7 | 50231706 | 13:82162818 | |
ARS-BFGL-NGS-31537 | 14 | 64995274 | 1 | 41315505 | 14:69103642 | |
1875855 | 15 | 29419479 | 20 | 46515729 | 15:31389253 | |
BTA-113745-no-rs | 15 | 81726795 | 2 | 12901670 | 2:15780878 | |
352984 | 18 | 57222022 | 4 | 66139068 | 18:57677863 | |
345202 | 18 | 64492276 | 7 | 93294065 | 18:64408080 | |
ARS-BFGL-NGS-77278 | 19 | 34916761 | 26 | 41917320 | 26:46541332 | |
ARS-BFGL-NGS-67396 | 19 | 55603678 | 20 | 10016943 | 19:54645063 | |
1859467 | 21 | 60422341 | 20 | 71596996 | 21:61747881 | |
ARS-BFGL-NGS-9612 | 21 | 64787627 | 10 | 40396512 | 21:66220013 | |
461240 | 22 | 54344094 | 17 | 31319897 | 22:53552948 | |
463748 | 22 | 60828419 | 11 | 84942870 | 22:59688782 | |
465954 | 23 | 42051287 | 17 | 42535225 | 23:41166590 | |
1860554 | 23 | 44428021 | 2 | 74386823 | 23:43645744 | |
BTA-58638-no-rs | 24 | 55379446 | 18 | 64455859 | 24:53790841 | |
ARS-BFGL-NGS-55374 | 25 | 28795159 | 9 | 43457907 | 9:42792078 | |
1860594 | 26 | 10984398 | 6 | 31957704 | 26:10567934 | |
ARS-BFGL-NGS-22409 | 26 | 32419852 | 19 | 41655298 | 19:43295532 | |
ARS-BFGL-NGS-102734 | 27 | 6298951 | 23 | 31511369 | 23:25899622 //23:26148979 | |
ARS-BFGL-NGS-40170 | 28 | 5149426 | 1 | 58990404 | 28:6888276 | |
1864508 | X | 48918943 | 8 | 45769443 | 8:42969739 | 5 |
ARS-BFGL-NGS-109695 | X | 48952760 | 8 | 46295084 | 8:43003529 | 5 |
1862184 | X | 48965834 | 8 | 46679390 | 8:43016396 | 5 |
BTB-01044512 | X | 48988556 | 8 | 45367300 | 8:43039113 | 5 |
BTB-01631465 | X | 67394831 | 26 | 30689907 | 26:32336734 | |
1862196 | X | 87059858 | 22 | 57016127 | X:146942067 | |
1863291 | X | 87885269 | 8 | 37568243 | X:138709703 | |
ARS-BFGL-NGS-10360 | X | 88338874 | 11 | 17475323 | X:137429436 | |