GWAS Details

GWAS Basic Information

GWAS_HUJI_winter16
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
3.16E-5
Mixed linear model (MLM)
R/GAPIT
Principal Components of the Genetic Similarity Matrix (PCA-GSM)
First, LDKNNi imputation of missing SNPs with default LD search for KNNi 10Mb, High LD Sites (l) 30 and Number of nearest neighbours (k) of 20. Second, TRADITOM_111K SNPsx1316acc was filtered to have only accession cultivated in HUJI_winter16. Only SNPs with MAF > 5% were used in the GWAS

GWAS Stat Test, Kinship Algorithm & Reference

t-Test
EMMA
TRADITOM_111K SNPsx1316acc
beta

1) https://doi.org/10.1093/hr/uhac112

Related Study Summary 1

Abbreviation Start Date End Date Location
HUJI_winter16 HUJI Hatzav fields

Related GWAS Variants Summary 79

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
SCCSL2.50ch00V1 g 0.056573705179283 1255 3.7829140293575E-5 0.029866106261777
SCCSL2.50ch05V1 g 0.070119521912351 1255 3.2954592522232E-5 0.029866106261777
FEC.brSL2.50ch02V1 c 0.065166795965865 1289 5.7556449418208E-9 4.5440816815675E-6
FEC.brSL2.50ch02V3 g 0.071761055081458 1289 1.6141785113186E-6 0.00084959595645737
FEC.brSL2.50ch05V1 g 0.11132660977502 1289 3.7002433161767E-9 4.5440816815675E-6
FEC.brSL2.50ch12V1 c 0.10589604344453 1289 3.4144012582424E-5 0.013478348966912
FEC.pkSL2.50ch01V1 c 0.16912335143522 1289 5.1410497891236E-24 8.1177176170261E-21
FEC.rdSL2.50ch01V2 c 0.16912335143522 1289 5.5295237168706E-15 8.7311179489386E-12
FEC.rdSL2.50ch11V1 c 0.079906904577192 1289 2.6300479341716E-6 0.0020764228440285
FEC.ylSL2.50ch03V4 g 0.069821567106284 1289 2.7301782097319E-5 0.021554756965833
FEC.ylSL2.50ch10V2 g 0.084949573312645 1289 2.1553767244464E-7 0.00034033398479008
FPS.bpSL2.50ch01V1 c 0.30687830687831 1134 4.7064993348523E-21 7.4315624497318E-18
FPS.bpSL2.50ch01V2 g 0.29938271604938 1134 3.7617033413405E-14 2.9698647879884E-11
FPS.bpSL2.50ch01V3 c 0.30908289241623 1134 8.5012970041767E-13 4.474515989865E-10
FPS.bpSL2.50ch02V1 g 0.078042328042328 1134 3.9045263078951E-6 0.00061652470401663
FPS.bpSL2.50ch02V4 c 0.085097001763668 1134 9.0602694839407E-6 0.0013005605013766
FPS.bpSL2.50ch04V2 c 0.078924162257496 1134 7.2563207456618E-8 1.9096217429E-5
FPS.bpSL2.50ch06V1 g 0.053350970017637 1134 1.2922980844894E-10 5.1013466885219E-8
FPS.bpSL2.50ch07V1 c 0.12169312169312 1134 2.6640574339506E-6 0.00046739407646755
FPS.bpSL2.50ch08V1 g 0.11199294532628 1134 6.6197511630453E-9 2.0905174172897E-6
FPS.bpSL2.50ch09V2 c 0.054673721340388 1134 8.7928437877244E-8 1.9834143344024E-5
FPS.bpSL2.50ch10V2 g 0.28350970017637 1134 5.5649851511014E-7 0.00010983889441986
FPS.bpSL2.50ch10V4 c 0.17680776014109 1134 3.0086529873152E-5 0.0039588858891422
FPS.flSL2.50ch02V1 g 0.31569664902998 1134 4.3151116837655E-9 6.8135613486657E-6
FPS.flSL2.50ch11V6 g 0.34215167548501 1134 1.4506858871768E-5 0.0089256905084802
FPS.flSL2.50ch11V7 c 0.35449735449735 1134 1.6958246691223E-5 0.0089256905084802
FPS.HtSL2.50ch08V2 g 0.055996472663139 1134 4.0377252491304E-7 0.00063755681683769
FPS.HtSL2.50ch08V5 g 0.055996472663139 1134 1.3139280540157E-5 0.0041493847945816
FPS.HtSL2.50ch08V8 t 0.056437389770723 1134 4.0708831013585E-6 0.0021426414723484
FPS.HtSL2.50ch08V11 g 0.070987654320988 1134 2.5615648316266E-6 0.0020223554345692
FPS.HtSL2.50ch10V1 g 0.070546737213404 1134 1.2518362277485E-5 0.0041493847945816
FPS.lgSL2.50ch00V2 c 0.068783068783069 1134 9.4733423576416E-7 0.0014958407582716
FPS.lgSL2.50ch02V3 t 0.12169312169312 1134 3.5100474081555E-5 0.018474549524925
FPS.lgSL2.50ch08V4 g 0.10582010582011 1134 1.6247903940424E-5 0.012827720160964
FPS.ovoSL2.50ch02V1 g 0.11640211640212 1134 1.8890438009992E-8 2.9828001617778E-5
FPS.ovoSL2.50ch10V1 g 0.21869488536155 1134 6.5633668816418E-6 0.0051817781530562
FPS.oxSL2.50ch03V2 c 0.057319223985891 1134 2.5635049854781E-5 0.0067462906201166
FPS.oxSL2.50ch03V3 c 0.064814814814815 1134 8.1139416610282E-8 6.4059569413817E-5
FPS.oxSL2.50ch05V2 g 0.058201058201058 1134 1.073897962009E-5 0.0033913697640244
FPS.oxSL2.50ch05V6 c 0.058641975308642 1134 5.5798593864533E-7 0.00029368659904033
FPS.oxSL2.50ch05V8 g 0.056878306878307 1134 3.7566897848831E-8 5.9318131703305E-5
FPS.oxSL2.50ch11V3 g 0.14726631393298 1134 3.302875722989E-6 0.0013038101916499
FPS.recSL2.50ch08V1 c 0.24955908289242 1134 2.9120276072706E-5 0.022990457959401
FPS.recSL2.50ch08V5 g 0.054232804232804 1134 3.1852761335725E-6 0.0050295510149109
FPS.rdSL2.50ch11V1 t 0.31393298059965 1134 2.3830338906057E-5 0.037628105132664
fasSL2.50ch02V1 g 0.31650570676032 1139 5.0940989186027E-7 0.00020108955481184
fasSL2.50ch11V1 t 0.31299385425812 1139 1.7927287917345E-11 2.8307187621488E-8
fasSL2.50ch11V4 g 0.34152765583846 1139 6.6382674677622E-10 5.2409121657983E-7
fasSL2.50ch11V7 c 0.35338015803336 1139 2.9479889376528E-9 1.5516248441846E-6
FShSSL2.50ch02V2 g 0.31539807524059 1143 8.2636657781545E-12 1.3048328263706E-8
FShSSL2.50ch11V1 t 0.31408573928259 1143 2.0152365549019E-8 1.5910292600951E-5
FShSSL2.50ch11V5 g 0.34339457567804 1143 4.4646598967709E-7 0.00023498993256671
FShSSL2.50ch11V9 c 0.35520559930009 1143 7.3542347495195E-6 0.0029030841673728
FWSL2.50ch11V1 t 0.31414868105516 1251 1.4051653201121E-12 7.3958534681899E-10
FWSL2.50ch11V6 g 0.34252597921663 1251 2.7842648697773E-15 4.3963542293783E-12
FWSL2.50ch11V12 c 0.35411670663469 1251 5.3162312780959E-13 4.1971645940567E-10
GHSL2.50ch01V1 g 0.073607932875667 1311 6.43298372876E-6 0.010157681307712
jpSL2.50ch00V7 g 0.10418482999128 1147 3.961188492401E-12 6.2547166295011E-9
jpSL2.50ch01V1 g 0.045771578029642 1147 1.8555122375589E-11 1.4649269115527E-8
jpSL2.50ch01V2 t 0.053182214472537 1147 1.4377186776512E-10 7.5671926400375E-8
jpSL2.50ch07V1 g 0.045335658238884 1147 1.6695428364395E-8 6.3348127136121E-6
jpSL2.50ch07V2 g 0.044899738448125 1147 2.0059571607385E-8 6.3348127136121E-6
LeSSL2.50ch08V1 c 0.06782946 1290 7.957013E-6 0.01256412
LSh.plSL2.50ch06V3 g 0.1771318 1290 2.737591E-5 0.02832784
LSh.dfSL2.50ch08V2 c 0.06782946 1290 5.42086E-7 0.0008559538
RCESL2.50ch02V1 g 0.3198587 1274 2.107198E-9 8.318166E-7
RCESL2.50ch11V1 t 0.3139717 1274 1.546385E-10 1.220871E-7
RCESL2.50ch11V3 g 0.3434066 1274 7.583956E-10 3.991689E-7
RCESL2.50ch11V6 c 0.3543956 1274 3.302516E-12 5.214672E-9
SkCSL2.50ch01V1 c 0.1695112 1289 1.495315E-23 2.361102E-20
SkCSL2.50ch01V4 g 0.4670287 1289 3.405301E-5 0.02688485
SPS.dtSL2.50ch02V1 g 0.3193574 1276 1.74391E-7 0.0001376817
SPS.dtSL2.50ch11V1 t 0.3142633 1276 7.402189E-8 0.0001168806
SPS.dtSL2.50ch11V3 g 0.3444357 1276 7.610002E-7 0.0004005398
SPS.irrSL2.50ch11V1 t 0.3142633 1276 1.60064E-7 0.0001263705
SPS.irrSL2.50ch11V3 g 0.3444357 1276 1.13433E-9 1.791107E-6
SPS.irrSL2.50ch11V4 c 0.3554075 1276 1.074503E-6 0.0005655469
SPS.lnSL2.50ch03V2 c 0.05916928 1276 4.208738E-7 0.0006645597
SPS.stSL2.50ch10V1 g 0.08816614 1276 3.169378E-5 0.05004448