GWAS Details

GWAS Basic Information

GWAS_INRA_summer15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
2.64E-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 INRA_summer15. 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
INRA_summer15 Avingnon_INRA

Related GWAS Variants Summary 153

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
arSL2.50ch01V1 g 0.39869281045752 153 1.3312141334114E-5 0.0083777742796027
arSL2.50ch11V1 t 0.30718954248366 153 1.8236227710435E-7 0.0001721499895865
arSL2.50ch11V5 c 0.34967320261438 153 2.2618561355879E-8 4.27038438399E-5
fic.aSL2.50ch03V1 A 0.052631578947368 152 8.184659595652E-7 0.0015452637316591
fic.bSL2.50ch10V1 T 0.14473684210526 152 1.9825537631255E-5 0.037430615047809
fic.HSL2.50ch03V1 A 0.052631578947368 152 9.1344447279501E-6 0.011261652022854
fic.HSL2.50ch03V2 A 0.059210526315789 152 1.7894574188858E-5 0.011261652022854
fic.HSL2.50ch03V3 T 0.059210526315789 152 1.7894574188858E-5 0.011261652022854
SCCSL2.50ch01V1 G 0.06329114 158 1.956503E-5 0.03693877
fse.curvedSL2.50ch00V2 c 0.05882353 153 9.078465E-10 1.714014E-6
fse.curvedSL2.50ch04V1 g 0.3496732 153 3.035203E-6 0.001910154
fse.curvedSL2.50ch05V1 c 0.0620915 153 1.980765E-7 0.0001869842
fse.curvedSL2.50ch05V4 c 0.09803922 153 1.846881E-5 0.006973821
fse.curvedSL2.50ch08V1 g 0.07189542 153 4.128977E-6 0.001948877
H.curvedSL2.50ch00V1 c 0.05882353 153 6.068519E-6 0.005728682
H.curvedSL2.50ch05V1 c 0.0620915 153 1.289825E-9 2.435189E-6
dan.macroSL2.50ch00V2 c 0.05882353 153 2.310863E-5 0.01454303
dan.macroSL2.50ch04V1 g 0.3496732 153 3.172435E-6 0.005989558
dan.macroSL2.50ch05V1 c 0.0620915 153 1.351255E-5 0.01275584
dblkSL2.50ch01V2 c 0.06862745 153 3.569071E-5 0.06738406
FEC.brSL2.50ch00V1 g 0.05345912 159 1.494173E-8 2.820998E-5
FEC.brSL2.50ch05V2 g 0.1823899 159 8.662847E-6 0.008177727
FEC.pkSL2.50ch03V1 g 0.172956 159 8.583157E-8 5.401667E-5
FEC.pkSL2.50ch05V1 c 0.05660377 159 1.776486E-5 0.005590008
FEC.pkSL2.50ch05V2 c 0.05345912 159 8.248993E-8 5.401667E-5
FEC.pkSL2.50ch05V3 g 0.05660377 159 3.381747E-8 5.401667E-5
FEC.pkSL2.50ch05V4 g 0.06289308 159 2.362363E-7 0.0001115036
FEC.pkSL2.50ch05V5 a 0.05345912 159 2.967393E-6 0.001120487
FEC.ppSL2.50ch01V1 g 0.07861635 159 1.025951E-6 0.001936996
FEC.ppSL2.50ch01V2 g 0.07232704 159 1.308664E-5 0.01212391
FEC.ppSL2.50ch11V1 c 0.1666667 159 2.592096E-5 0.01212391
FEC.rdSL2.50ch03V1 g 0.172956 159 1.051401E-7 0.0001985045
FEC.ylSL2.50ch03V1 a 0.05031447 159 3.724898E-7 0.000389162
FEC.ylSL2.50ch03V2 a 0.05660377 159 2.413295E-6 0.001139075
FEC.ylSL2.50ch03V3 t 0.05660377 159 2.413295E-6 0.001139075
FEC.ylSL2.50ch12V1 a 0.05031447 159 1.484095E-5 0.005603944
FEC.ylSL2.50ch12V2 g 0.05031447 159 4.122479E-7 0.000389162
ellSL2.50ch11V3 c 0.3496732 153 6.877766E-6 0.01298522
fec.aSL2.50ch03V1 a 0.05063291 158 1.023936E-7 0.0001933191
fec.aSL2.50ch03V2 a 0.05696203 158 1.536949E-6 0.0009672534
fec.aSL2.50ch03V3 t 0.05696203 158 1.536949E-6 0.0009672534
fec.aSL2.50ch12V1 g 0.05063291 158 4.188903E-6 0.001977162
fec.LSL2.50ch09V1 c 0.05063291 158 3.697561E-5 0.06980995
FPS.bpSL2.50ch02V3 c 0.08227848 158 1.843535E-7 0.0003187788
FPS.bpSL2.50ch04V3 c 0.0664557 158 2.399951E-6 0.001234551
FPS.bpSL2.50ch04V4 c 0.05379747 158 3.376894E-7 0.0003187788
FPS.bpSL2.50ch09V3 c 0.06329114 158 2.615573E-6 0.001234551
FPS.bpSL2.50ch10V3 g 0.07594937 158 4.87859E-6 0.001556489
FPS.bpSL2.50ch11V1 c 0.08544304 158 2.967358E-5 0.008003389
FPS.bpSL2.50ch11V2 c 0.07911392 158 4.946471E-6 0.001556489
FPS.flSL2.50ch11V3 t 0.3291139 158 1.577161E-5 0.0148884
FPS.flSL2.50ch11V5 g 0.3512658 158 8.995444E-6 0.0148884
FPS.lgSL2.50ch00V1 c 0.06012658 158 5.245688E-8 9.90386E-5
FPS.lgSL2.50ch09V1 g 0.1075949 158 1.242064E-6 0.001172509
FPS.ovoSL2.50ch02V2 g 0.1012658 158 2.884466E-6 0.005445871
FPS.oxSL2.50ch03V1 g 0.06962025 158 2.360318E-5 0.01485427
FPS.oxSL2.50ch05V9 g 0.09177215 158 6.314453E-7 0.001192169
FPS.oxSL2.50ch11V4 g 0.1708861 158 8.718606E-6 0.008230364
FPS.rdSL2.50ch11V2 c 0.3670886 158 1.393205E-5 0.02630372
fse.ISL2.50ch00V2 c 0.05882353 153 3.566223E-9 6.73303E-6
fse.ISL2.50ch04V1 g 0.3496732 153 3.28534E-6 0.002067574
fse.ISL2.50ch05V1 c 0.0620915 153 1.383054E-6 0.001305603
fse.ISL2.50ch08V3 g 0.07189542 153 1.786015E-5 0.008429991
fse.IISL2.50ch00V2 c 0.05882353 153 4.479755E-8 8.457777E-5
fse.IISL2.50ch04V1 g 0.3496732 153 3.716303E-6 0.002338794
fse.IISL2.50ch05V1 c 0.0620915 153 2.10551E-6 0.001987602
fse.IISL2.50ch08V1 g 0.07189542 153 2.439158E-5 0.01151283
fsiSL2.50ch00V2 c 0.05882353 153 1.755422E-8 3.314237E-5
fsiSL2.50ch04V1 g 0.3496732 153 4.15233E-6 0.003919799
fsiSL2.50ch05V1 c 0.0620915 153 8.938812E-6 0.005625492
fsiSL2.50ch08V1 g 0.07189542 153 2.032171E-5 0.009591848
FShSSL2.50ch02V1 g 0.4240506 158 3.788495E-5 0.0178817
FShSSL2.50ch11V4 t 0.3291139 158 2.425091E-5 0.01712888
FShSSL2.50ch11V6 g 0.3512658 158 2.721749E-5 0.01712888
FShSSL2.50ch11V8 c 0.3670886 158 7.047801E-6 0.01330625
FWSL2.50ch11V2 t 0.3291139 158 1.571262E-6 0.002537264
FWSL2.50ch11V9 g 0.3512658 158 4.031669E-6 0.002537264
FWSL2.50ch11V14 c 0.3670886 158 3.504162E-6 0.002537264
H.midSL2.50ch00V3 c 0.05882353 153 1.380077E-5 0.01302793
H.midSL2.50ch05V1 c 0.0620915 153 3.339425E-10 6.304835E-7
jpSL2.50ch00V2 g 0.4025157 159 2.128447E-5 0.002679005
jpSL2.50ch00V3 c 0.4025157 159 2.128447E-5 0.002679005
jpSL2.50ch01V3 t 0.05031447 159 1.206682E-5 0.001898513
jpSL2.50ch02V1 a 0.05031447 159 2.632988E-6 0.0007101544
jpSL2.50ch02V2 g 0.05031447 159 2.632988E-6 0.0007101544
jpSL2.50ch02V3 a 0.05031447 159 2.632988E-6 0.0007101544
jpSL2.50ch03V3 g 0.05031447 159 2.593541E-5 0.003060379
jpSL2.50ch05V6 t 0.05031447 159 1.201219E-5 0.001898513
jpSL2.50ch05V7 g 0.05974843 159 3.910977E-6 0.0008394208
jpSL2.50ch05V8 c 0.07232704 159 3.546426E-5 0.003938619
jpSL2.50ch06V4 a 0.05031447 159 1.127421E-6 0.0007101544
jpSL2.50ch07V3 t 0.05031447 159 1.305442E-6 0.0007101544
jpSL2.50ch09V1 c 0.05031447 159 4.096198E-7 0.0007101544
jpSL2.50ch09V2 t 0.05345912 159 4.001476E-6 0.0008394208
jpSL2.50ch11V2 g 0.06289308 159 4.726592E-6 0.0008923806
jpSL2.50ch11V5 c 0.08176101 159 1.80757E-5 0.002625147
jpSL2.50ch11V7 g 0.07232704 159 2.353612E-6 0.0007101544
lcnSL2.50ch11V3 t 0.3291139 158 1.612386E-9 1.522093E-6
lcnSL2.50ch11V7 g 0.3512658 158 3.479542E-9 2.189792E-6
lcnSL2.50ch11V12 c 0.3670886 158 1.912116E-10 3.610075E-7
lcnSL2.50ch11V18 g 0.443038 158 1.410974E-5 0.006659798
LSh.plSL2.50ch04V2 g 0.05974843 159 3.497147E-5 0.004716153
LSh.plSL2.50ch04V3 g 0.05974843 159 1.749331E-5 0.003188843
LSh.plSL2.50ch04V4 c 0.05660377 159 2.520911E-5 0.003661139
LSh.plSL2.50ch04V5 c 0.05660377 159 1.758096E-5 0.003188843
LSh.plSL2.50ch04V6 t 0.05974843 159 1.973067E-5 0.003188843
LSh.plSL2.50ch04V7 g 0.05031447 159 1.935757E-6 0.00231468
LSh.plSL2.50ch04V8 c 0.05345912 159 8.581972E-6 0.00231468
LSh.plSL2.50ch04V9 g 0.05345912 159 8.581972E-6 0.00231468
LSh.plSL2.50ch04V10 g 0.05345912 159 8.581972E-6 0.00231468
LSh.plSL2.50ch04V11 c 0.05345912 159 8.581972E-6 0.00231468
LSh.plSL2.50ch04V12 g 0.05345912 159 8.581972E-6 0.00231468
LSh.plSL2.50ch04V13 g 0.1446541 159 1.036848E-5 0.002446962
LSh.plSL2.50ch04V14 t 0.06603774 159 6.471028E-6 0.00231468
LSh.plSL2.50ch08V1 g 0.05660377 159 2.026807E-5 0.003188843
LSh.rlSL2.50ch04V2 g 0.05031447 159 2.72752E-5 0.02680319
H.maxSL2.50ch00V1 c 0.05882353 153 8.272956E-6 0.007809671
H.maxSL2.50ch05V1 c 0.0620915 153 1.313126E-9 2.479182E-6
W.maxSL2.50ch11V1 t 0.3071895 153 9.454342E-8 8.924899E-5
W.maxSL2.50ch11V5 g 0.3267974 153 3.949164E-6 0.00248534
W.maxSL2.50ch11V7 c 0.3496732 153 1.142535E-9 2.157106E-6
osiSL2.50ch08V1 g 0.06535948 153 2.718324E-5 0.02060607
osiSL2.50ch08V2 g 0.06535948 153 2.718324E-5 0.02060607
osiSL2.50ch08V3 a 0.05555556 153 3.274269E-5 0.02060607
perSL2.50ch01V1 g 0.3986928 153 1.276518E-5 0.008033556
perSL2.50ch01V2 c 0.4019608 153 2.648145E-5 0.01050334
perSL2.50ch01V3 c 0.4019608 153 2.781605E-5 0.01050334
perSL2.50ch11V1 t 0.3071895 153 5.423702E-7 0.0005119975
perSL2.50ch11V6 c 0.3496732 153 4.301465E-8 8.121166E-5
PUFSL2.50ch00V1 c 0.06089744 156 4.019357E-9 7.588545E-6
PUFSL2.50ch00V2 a 0.08974359 156 2.357811E-5 0.01155038
PUFSL2.50ch08V1 c 0.1314103 156 1.703855E-5 0.01155038
PUFSL2.50ch08V2 g 0.05769231 156 2.447114E-5 0.01155038
recSL2.50ch05V1 c 0.0620915 153 1.063723E-6 0.00200831
recSL2.50ch05V2 c 0.09803922 153 2.975352E-5 0.02808733
RCESL2.50ch11V2 t 0.3291139 158 8.133152E-7 0.0007677696
RCESL2.50ch11V4 g 0.3512658 158 9.415838E-6 0.005925701
RCESL2.50ch11V7 c 0.3670886 158 3.356688E-7 0.0006337427
pshSL2.50ch00V1 g 0.09477124 153 2.553855E-5 0.04821678
SkCSL2.50ch03V1 g 0.1677215 158 3.492619E-6 0.002198021
SkCSL2.50ch05V1 c 0.05379747 158 3.162895E-6 0.002198021
SkCSL2.50ch05V2 g 0.05696203 158 1.728524E-6 0.002198021
SkCSL2.50ch05V3 g 0.06329114 158 4.859246E-6 0.002293564
SPS.dtSL2.50ch11V2 t 0.3291139 158 2.416931E-5 0.02281583
SPS.dtSL2.50ch11V6 c 0.3670886 158 2.134155E-5 0.02281583
SPS.irrSL2.50ch11V2 t 0.3291139 158 7.678164E-6 0.01449637
SPS.lnSL2.50ch02V1 t 0.1835443 158 3.168985E-5 0.0469637
par.RSL2.50ch02V2 g 0.2385621 153 5.156803E-6 0.004868022
par.RSL2.50ch11V2 t 0.3071895 153 7.864432E-6 0.004949349
par.RSL2.50ch11V6 c 0.3496732 153 1.61471E-6 0.003048573
W.midSL2.50ch11V1 t 0.3071895 153 1.634322E-7 0.00015428
W.midSL2.50ch11V6 g 0.3267974 153 7.078505E-6 0.004454739
W.midSL2.50ch11V7 c 0.3496732 153 2.495137E-9 4.710818E-6