GWAS Details

GWAS Basic Information

GWAS_ARCA2010_summer15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
2.89E-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 ARCA2010_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
ARCA2010_summer15 ARCA 2010 Societa Cooperativa A.r.l.

Related GWAS Variants Summary 113

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
arSL2.50ch05V1 A 0.059210526315789 228 1.1967922420786E-5 0.024965086169759
fse.curvedSL2.50ch02V1 g 0.36622807017544 228 2.0913739792508E-8 4.3626061207171E-5
dan.macroSL2.50ch02V1 g 0.36622807017544 228 3.9743708004226E-10 8.2905374896815E-7
decSL2.50ch01V2 t 0.054824561403509 228 1.4682650477379E-6 0.0030628008895812
dblkSL2.50ch00V1 A 0.067982456140351 228 1.9931821230723E-5 0.020788889543644
dblkSL2.50ch10V1 t 0.072368421052631 228 1.0013157283956E-5 0.020788889543644
desiSL2.50ch01V3 t 0.054824561403509 228 1.2712255064647E-7 0.00026517764064853
eccSL2.50ch02V2 g 0.36622807017544 228 5.6582520865775E-10 1.1803113852601E-6
eccSL2.50ch11V2 t 0.14912280701754 228 3.3243298169648E-6 0.0034672759990943
eccSL2.50ch11V6 g 0.14254385964912 228 3.011925212227E-5 0.020896501773023
eaiSL2.50ch02V1 g 0.36622807017544 228 1.909179859128E-9 3.982549186141E-6
eaiSL2.50ch08V1 g 0.094298245614035 228 4.6612698921278E-6 0.0048617044974893
FEC.orSL2.50ch02V1 t 0.05 230 1.6262880071942E-7 0.00033924367830072
FEC.pkSL2.50ch01V4 c 0.27173913043478 230 2.9525874310913E-5 0.061590973812566
FEC.rdSL2.50ch02V1 t 0.05 230 3.7745625398458E-5 0.078737374581182
FPS.ellSL2.50ch08V1 g 0.10652173913044 230 2.0602741178327E-6 0.004297731809799
FPS.flSL2.50ch02V2 g 0.37173913043478 230 1.4756621944974E-6 0.0030782313377215
FPS.HtSL2.50ch04V1 c 0.13695652173913 230 1.4359257960688E-6 0.0029953412105995
FPS.lgSL2.50ch02V1 a 0.054347826086956 230 3.7977009322711E-6 0.0039610020723588
FPS.lgSL2.50ch03V1 c 0.12173913043478 230 2.6940659664288E-7 0.00056198216059705
FPS.lgSL2.50ch04V2 a 0.095652173913043 230 3.0789973136146E-5 0.021409294654
FPS.ovoSL2.50ch06V2 g 0.11304347826087 230 1.2353981582366E-5 0.025770405580816
FPS.oxSL2.50ch04V2 g 0.058695652173913 230 3.4940684060116E-5 0.01822156673735
FPS.oxSL2.50ch11V5 c 0.15434782608696 230 3.3798227507239E-6 0.00705031025801
FPS.oxSL2.50ch12V1 g 0.058695652173913 230 2.3582735770425E-5 0.016397862272369
FPS.oxSL2.50ch12V2 g 0.058695652173913 230 2.3582735770425E-5 0.016397862272369
FPS.recSL2.50ch03V1 g 0.05 230 2.2074130567998E-5 0.023023318182422
FPS.recSL2.50ch05V1 c 0.052173913043478 230 2.8845807405449E-6 0.0060172354247766
fasSL2.50ch04V1 g 0.1304348 230 3.275355E-5 0.01708098
fasSL2.50ch11V2 t 0.1478261 230 1.007505E-8 2.101656E-5
fasSL2.50ch11V5 g 0.1413043 230 2.131405E-7 0.0002223056
fasSL2.50ch11V9 c 0.1543478 230 7.091706E-7 0.00049311
fse.ISL2.50ch02V1 g 0.36622807017544 228 2.7722708362534E-8 5.7829569644245E-5
fse.IISL2.50ch02V1 g 0.36622807017544 228 3.7970904580054E-9 7.9207306953992E-6
fsiSL2.50ch02V1 g 0.36622807017544 228 3.6666920341485E-9 7.6487195832338E-6
FShSSL2.50ch02V3 g 0.3717391 230 3.747332E-6 0.007816935
FShSSL2.50ch08V1 g 0.09347826 230 1.582158E-5 0.01100127
FShSSL2.50ch11V2 t 0.1478261 230 1.11041E-5 0.01100127
FWSL2.50ch05V1 c 0.05482456 228 1.656124E-5 0.009271963
FWSL2.50ch05V2 a 0.05921053 228 2.370938E-5 0.009891554
FWSL2.50ch05V3 g 0.05701754 228 1.628526E-5 0.009271963
FWSL2.50ch11V4 t 0.1491228 228 2.944368E-6 0.006141952
FWSL2.50ch11V10 g 0.1425439 228 1.777941E-5 0.009271963
lobSL2.50ch11V1 t 0.1491228 228 2.281472E-7 0.0004759152
lcnSL2.50ch02V1 g 0.3662281 228 1.149335E-5 0.005993783
lcnSL2.50ch11V1 t 0.1491228 228 1.865936E-12 3.892343E-9
lcnSL2.50ch11V6 g 0.1425439 228 2.550953E-9 1.773762E-6
lcnSL2.50ch11V13 c 0.1557018 228 1.622345E-9 1.692106E-6
W.maxSL2.50ch02V2 g 0.3662281 228 7.23251E-7 0.001419297
W.maxSL2.50ch11V3 t 0.1491228 228 1.360783E-6 0.001419297
W.maxSL2.50ch11V6 g 0.1425439 228 1.417034E-5 0.00985311
perSL2.50ch05V1 a 0.05921053 228 2.332469E-6 0.004865531
perSL2.50ch11V3 t 0.1491228 228 1.451731E-5 0.01514155
pan.macroSL2.50ch02V1 g 0.3662281 228 2.664185E-10 5.55749E-7
pan.microSL2.50ch12V1 t 0.4429825 228 3.766006E-5 0.07855888
pecSL2.50ch03V1 t 0.0504386 228 3.159556E-5 0.06590834
piarSL2.50ch02V1 g 0.3662281 228 7.17198E-8 0.0001496075
piarSL2.50ch05V2 t 0.1907895 228 2.951003E-6 0.003077896
piarSL2.50ch11V3 t 0.1491228 228 6.442528E-6 0.004479704
pshSL2.50ch02V1 g 0.3662281 228 9.401486E-10 1.96115E-6
pshSL2.50ch05V1 t 0.1907895 228 1.559875E-6 0.00162695
pshSL2.50ch11V2 t 0.1491228 228 1.907205E-5 0.01326143
SkCSL2.50ch05V4 c 0.07826087 230 1.515958E-5 0.03162288
SPS.irrSL2.50ch08V1 g 0.09513274 226 1.897407E-5 0.0395799
SPS.lnSL2.50ch00V1 c 0.04867257 226 8.104198E-10 1.690536E-7
SPS.lnSL2.50ch02V2 c 0.05973451 226 1.865697E-6 0.0001468204
SPS.lnSL2.50ch02V3 g 0.05309735 226 1.90036E-6 0.0001468204
SPS.lnSL2.50ch02V4 c 0.05309735 226 1.90036E-6 0.0001468204
SPS.lnSL2.50ch03V1 g 0.05088496 226 1.411123E-5 0.0008410296
SPS.lnSL2.50ch04V1 c 0.06637168 226 8.523458E-6 0.0005387859
SPS.lnSL2.50ch04V2 c 0.06637168 226 8.523458E-6 0.0005387859
SPS.lnSL2.50ch04V3 g 0.05973451 226 2.601398E-7 2.359355E-5
SPS.lnSL2.50ch04V4 g 0.05752212 226 3.125769E-10 1.043592E-7
SPS.lnSL2.50ch04V5 c 0.05752212 226 3.125769E-10 1.043592E-7
SPS.lnSL2.50ch04V6 g 0.07300885 226 4.62479E-6 0.0003112036
SPS.lnSL2.50ch04V7 g 0.05973451 226 4.502553E-10 1.043592E-7
SPS.lnSL2.50ch04V8 c 0.0619469 226 2.617319E-6 0.0001949902
SPS.lnSL2.50ch04V9 g 0.05973451 226 8.635563E-8 8.188084E-6
SPS.lnSL2.50ch04V10 c 0.05752212 226 3.834004E-9 5.688568E-7
SPS.lnSL2.50ch04V11 g 0.05752212 226 2.651583E-11 1.843734E-8
SPS.lnSL2.50ch04V12 g 0.06637168 226 1.116773E-6 9.706617E-5
SPS.lnSL2.50ch05V1 g 0.05973451 226 4.090533E-9 5.688568E-7
SPS.lnSL2.50ch05V2 t 0.0619469 226 1.517656E-9 2.435254E-7
SPS.lnSL2.50ch05V3 g 0.05973451 226 3.763809E-10 1.043592E-7
SPS.lnSL2.50ch05V4 c 0.05752212 226 5.239383E-9 6.830845E-7
SPS.lnSL2.50ch05V5 c 0.05973451 226 1.617112E-8 1.874053E-6
SPS.lnSL2.50ch05V6 g 0.0619469 226 1.517656E-9 2.435254E-7
SPS.lnSL2.50ch05V8 g 0.05530973 226 3.913572E-6 0.0002721237
SPS.lnSL2.50ch05V9 c 0.05530973 226 3.913572E-6 0.0002721237
SPS.lnSL2.50ch05V10 c 0.05973451 226 3.777356E-8 3.752173E-6
SPS.lnSL2.50ch05V11 g 0.0619469 226 2.737343E-8 3.005315E-6
SPS.lnSL2.50ch05V12 c 0.05973451 226 3.777356E-8 3.752173E-6
SPS.lnSL2.50ch05V13 g 0.05309735 226 4.150087E-10 1.043592E-7
SPS.lnSL2.50ch05V16 g 0.05752212 226 8.47802E-14 8.842575E-11
SPS.lnSL2.50ch05V17 c 0.05752212 226 8.47802E-14 8.842575E-11
SPS.lnSL2.50ch05V18 g 0.05309735 226 1.257564E-8 1.543105E-6
SPS.lnSL2.50ch05V19 t 0.05752212 226 9.79102E-10 1.856733E-7
SPS.lnSL2.50ch05V20 g 0.05309735 226 2.168038E-10 1.043592E-7
SPS.lnSL2.50ch12V1 c 0.05088496 226 1.339406E-5 0.0008217652
SPS.stSL2.50ch01V2 c 0.07300885 226 1.649741E-5 0.0344136
par.RSL2.50ch02V1 g 0.3662281 228 1.944199E-7 0.0004055599
par.RSL2.50ch11V1 t 0.1491228 228 7.227257E-6 0.005025352
par.RSL2.50ch11V4 g 0.1425439 228 1.796405E-6 0.00187365
par.RSL2.50ch11V9 c 0.1557018 228 1.732087E-5 0.009032836
ptk.RSL2.50ch11V1 t 0.1491228 228 9.954414E-7 0.001148314
ptk.RSL2.50ch11V2 g 0.1425439 228 1.100972E-6 0.001148314
verSL2.50ch02V1 g 0.3662281 228 2.317554E-5 0.01208604
verSL2.50ch11V1 t 0.1491228 228 6.328434E-6 0.006600557
verSL2.50ch11V4 g 0.1425439 228 1.241425E-5 0.008632045
verSL2.50ch12V1 g 0.06578947 228 7.138761E-7 0.001489146
W.midSL2.50ch02V1 g 0.3662281 228 9.517034E-8 0.0001985253
W.midSL2.50ch11V2 t 0.1491228 228 3.559052E-7 0.0003712091
W.midSL2.50ch11V5 g 0.1425439 228 5.103937E-6 0.003548938