GWAS Details

GWAS Basic Information

GWAS_PERELLO_summer15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
3.12E-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 PERELLO_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
PERELLO_summer15 Coop. V. Unión Protectora del Perelló

Related GWAS Variants Summary 159

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
arSL2.50ch06V1 g 0.16824644549763 211 2.1518882017395E-5 0.014879311566339
arSL2.50ch11V3 t 0.41943127962085 211 2.793362621966E-5 0.014879311566339
arSL2.50ch11V4 g 0.38862559241706 211 1.0124241594991E-5 0.014879311566339
fse.curvedSL2.50ch01V1 G 0.056872037914692 211 2.4449340626567E-5 0.013023348773751
fse.curvedSL2.50ch08V4 c 0.082938388625592 211 1.4924364806638E-5 0.011924567480504
fse.curvedSL2.50ch08V5 g 0.071090047393365 211 6.200792017965E-11 9.9088656447081E-8
H.curvedSL2.50ch08V1 g 0.071090047393365 211 5.7791565876106E-7 0.00092350922270018
dan.macroSL2.50ch08V1 c 0.09478672985782 211 1.8357100046729E-5 0.014667322937337
dan.macroSL2.50ch08V3 g 0.071090047393365 211 8.8411433999511E-7 0.0014128147153122
dblkSL2.50ch01V1 c 0.052132701421801 211 5.7539530225431E-6 0.004597408465012
dblkSL2.50ch08V1 g 0.10663507109005 211 2.4089815190163E-5 0.01283184155796
dblkSL2.50ch08V2 g 0.071090047393365 211 4.6416419597187E-7 0.00074173438516305
desiSL2.50ch08V1 c 0.09478672985782 211 2.8957598126437E-5 0.013861342187457
desiSL2.50ch08V2 c 0.10663507109005 211 3.4696726376614E-5 0.013861342187457
desiSL2.50ch08V3 c 0.11137440758294 211 3.2927076851563E-5 0.013861342187457
desiSL2.50ch08V4 g 0.071090047393365 211 1.7979027855212E-9 2.8730486512629E-6
eccSL2.50ch02V3 g 0.19905213270142 211 1.2518610288597E-5 0.0066682464137258
eccSL2.50ch11V3 t 0.41943127962085 211 1.6701907601544E-5 0.0066724120868167
eccSL2.50ch11V4 g 0.38862559241706 211 3.1278564523609E-7 0.00049983146108727
eccSL2.50ch11V7 c 0.3696682464455 211 5.2775654096865E-6 0.0042167747623395
eaiSL2.50ch02V2 g 0.19905213270142 211 7.1889374562704E-6 0.01148792205512
eaiSL2.50ch11V2 g 0.38862559241706 211 2.1168208518458E-5 0.016913398606248
FEC.brSL2.50ch02V2 c 0.11611374407583 211 1.0520057960423E-5 0.016811052620755
FEC.brSL2.50ch02V4 g 0.1042654028436 211 2.9582326858872E-5 0.023636279160239
FEC.orSL2.50ch03V2 g 0.052132701421801 211 7.0564057280243E-6 0.0037587121177943
FEC.orSL2.50ch03V3 a 0.054502369668246 211 2.7742719700405E-6 0.0031116748021726
FEC.orSL2.50ch03V4 t 0.052132701421801 211 3.8944615796904E-6 0.0031116748021726
FEC.orSL2.50ch09V1 c 0.061611374407583 211 1.9017356887083E-5 0.0075974340763898
FEC.rdSL2.50ch01V1 g 0.07109005 211 3.405751E-5 0.0544239
FEC.ylSL2.50ch02V1 t 0.09952607 211 6.978725E-6 0.005576001
FEC.ylSL2.50ch02V2 a 0.1018957 211 1.270696E-5 0.006768574
FEC.ylSL2.50ch02V3 t 0.0971564 211 5.456186E-6 0.005576001
ellSL2.50ch11V1 g 0.3886256 211 4.433776E-6 0.007085174
ellSL2.50ch11V5 c 0.3696682 211 1.210516E-5 0.009672025
FPS.ellSL2.50ch01V1 g 0.05687204 211 3.218483E-6 0.005143136
FPS.ellSL2.50ch06V1 t 0.05924171 211 1.240497E-5 0.009911573
FPS.ellSL2.50ch08V2 c 0.0971564 211 3.48713E-5 0.01857478
FPS.lgSL2.50ch01V1 g 0.05687204 211 1.37201E-5 0.002740589
FPS.lgSL2.50ch04V1 t 0.06398104 211 4.774074E-6 0.001529552
FPS.lgSL2.50ch06V3 c 0.09478673 211 4.785832E-6 0.001529552
FPS.lgSL2.50ch08V1 c 0.09478673 211 1.046267E-5 0.002388477
FPS.lgSL2.50ch08V3 g 0.05924171 211 8.74248E-6 0.002328414
FPS.lgSL2.50ch08V6 g 0.05450237 211 5.228763E-8 2.785188E-5
FPS.lgSL2.50ch08V7 c 0.08293839 211 1.797904E-5 0.003192279
FPS.lgSL2.50ch08V8 g 0.07109005 211 4.378759E-9 3.498628E-6
FPS.lgSL2.50ch09V2 t 0.07582938 211 3.562079E-9 3.498628E-6
FPS.ovoSL2.50ch03V2 c 0.1113744 211 9.150079E-6 0.01008445
FPS.ovoSL2.50ch08V1 g 0.1066351 211 1.262134E-5 0.01008445
FPS.oxSL2.50ch04V1 a 0.1611374 211 6.008468E-6 0.009601533
FPS.recSL2.50ch08V2 c 0.0521327 211 1.221264E-6 0.0006505266
FPS.recSL2.50ch08V3 g 0.0521327 211 5.666415E-7 0.0004527466
FPS.recSL2.50ch08V4 g 0.0521327 211 5.666415E-7 0.0004527466
fasSL2.50ch11V11 c 0.3696682 211 3.931637E-6 0.006282757
fse.ISL2.50ch06V3 c 0.09478673 211 3.319979E-5 0.01347202
fse.ISL2.50ch08V1 c 0.09478673 211 3.597697E-5 0.01347202
fse.ISL2.50ch08V6 c 0.08293839 211 2.156615E-5 0.01347202
fse.ISL2.50ch08V7 g 0.07109005 211 1.413215E-10 2.258317E-7
fse.IISL2.50ch06V3 c 0.09478673 211 2.76415E-5 0.01700609
fse.IISL2.50ch08V5 g 0.07109005 211 5.196736E-10 8.304385E-7
fsiSL2.50ch06V3 c 0.09478673 211 2.317881E-5 0.01851987
fsiSL2.50ch08V5 g 0.07109005 211 6.426687E-10 1.026985E-6
triSL2.50ch01V3 c 0.0521327 211 1.184362E-6 0.0006308704
triSL2.50ch08V1 g 0.1066351 211 7.436296E-7 0.0005941601
triSL2.50ch08V2 g 0.07109005 211 2.247435E-8 3.591402E-5
triSL2.50ch08V3 c 0.0521327 211 1.10536E-5 0.004415914
FShSSL2.50ch11V3 t 0.4194313 211 1.924493E-5 0.02465118
FShSSL2.50ch11V7 g 0.3886256 211 3.085254E-5 0.02465118
FWSL2.50ch02V1 g 0.1990521 211 3.429009E-5 0.01369889
FWSL2.50ch11V3 t 0.4194313 211 2.692673E-6 0.002151445
FWSL2.50ch11V7 g 0.3886256 211 3.857572E-7 0.00061644
FWSL2.50ch11V15 c 0.3696682 211 7.668202E-6 0.004084596
GShSL2.50ch10V1 g 0.06872038 211 9.324889E-6 0.01490117
GHSL2.50ch03V1 a 0.1090047 211 7.044365E-9 1.12569E-5
GHSL2.50ch04V1 g 0.0521327 211 2.889592E-5 0.003847973
GHSL2.50ch04V2 g 0.0521327 211 1.862291E-5 0.002975941
GHSL2.50ch04V3 c 0.0521327 211 1.862291E-5 0.002975941
GHSL2.50ch07V1 a 0.0521327 211 9.72859E-6 0.002220898
GHSL2.50ch07V2 t 0.05450237 211 2.29366E-5 0.003332062
GHSL2.50ch10V1 c 0.06161137 211 4.187011E-6 0.001672711
GHSL2.50ch11V1 c 0.06161137 211 2.094247E-6 0.001115535
GHSL2.50ch11V2 a 0.05924171 211 1.008162E-6 0.0008055211
GHSL2.50ch11V3 g 0.06161137 211 9.225719E-6 0.002220898
GHSL2.50ch11V4 c 0.06161137 211 9.225719E-6 0.002220898
GHSL2.50ch12V1 g 0.1090047 211 1.560251E-5 0.002975941
H.midSL2.50ch08V1 g 0.07109005 211 5.561913E-9 8.887937E-6
jpSL2.50ch00V1 g 0.4549763 211 1.577956E-7 6.303934E-5
jpSL2.50ch00V4 g 0.4691943 211 1.627407E-5 0.0009287845
jpSL2.50ch00V5 g 0.1066351 211 1.790449E-6 0.0001788211
jpSL2.50ch04V2 t 0.0521327 211 1.944812E-5 0.001035937
jpSL2.50ch04V3 t 0.06635071 211 8.159204E-6 0.000543267
jpSL2.50ch05V2 t 0.05924171 211 3.844956E-6 0.0003614259
jpSL2.50ch05V3 g 0.06398104 211 2.676446E-5 0.001379665
jpSL2.50ch05V5 c 0.0521327 211 6.959726E-7 0.0001112164
jpSL2.50ch06V1 c 0.1184834 211 4.89002E-6 0.0004341251
jpSL2.50ch06V2 g 0.0971564 211 1.194645E-6 0.0001590869
jpSL2.50ch06V3 g 0.1184834 211 6.684553E-6 0.000466685
jpSL2.50ch06V5 c 0.1090047 211 1.492207E-5 0.0009072638
jpSL2.50ch06V6 g 0.1042654 211 6.280732E-6 0.000466685
jpSL2.50ch08V1 c 0.0521327 211 1.532924E-5 0.0009072638
jpSL2.50ch11V1 c 0.06635071 211 1.553917E-6 0.0001788211
jpSL2.50ch11V3 g 0.06635071 211 3.071208E-5 0.001533685
jpSL2.50ch11V4 c 0.06872038 211 1.55996E-9 1.246408E-6
jpSL2.50ch11V6 g 0.06635071 211 1.343941E-10 2.147617E-7
jpSL2.50ch11V8 c 0.06161137 211 2.42063E-7 7.394812E-5
jpSL2.50ch11V10 c 0.06635071 211 1.225749E-5 0.0007834987
jpSL2.50ch11V11 g 0.06161137 211 5.898815E-6 0.000466685
jpSL2.50ch11V12 c 0.06161137 211 5.898815E-6 0.000466685
jpSL2.50ch11V13 c 0.05450237 211 3.561604E-5 0.00172468
jpSL2.50ch11V14 g 0.05450237 211 4.532397E-7 8.047522E-5
jpSL2.50ch11V15 g 0.05450237 211 4.532397E-7 8.047522E-5
jpSL2.50ch11V17 c 0.05924171 211 1.704091E-6 0.0001788211
jpSL2.50ch11V18 t 0.05687204 211 1.716256E-6 0.0001788211
jpSL2.50ch11V22 a 0.08293839 211 1.789755E-5 0.0009862166
jpSL2.50ch11V23 t 0.07582938 211 8.727032E-7 0.00012678
jpSL2.50ch11V24 a 0.07819905 211 6.716993E-6 0.000466685
jpSL2.50ch11V25 a 0.07345972 211 1.40029E-7 6.303934E-5
jpSL2.50ch11V26 a 0.07819905 211 3.23928E-7 7.394812E-5
jpSL2.50ch11V27 g 0.07819905 211 3.23928E-7 7.394812E-5
lcnSL2.50ch02V2 g 0.1990521 211 1.482871E-5 0.004531957
lcnSL2.50ch06V1 c 0.1729858 211 1.701611E-5 0.004531957
lcnSL2.50ch11V4 t 0.4194313 211 1.897958E-8 1.851947E-5
lcnSL2.50ch11V8 g 0.3886256 211 2.317831E-8 1.851947E-5
lcnSL2.50ch11V15 c 0.3696682 211 7.738841E-8 4.122223E-5
lcnSL2.50ch11V17 g 0.3767773 211 4.538219E-6 0.001813018
LSh.plSL2.50ch07V1 g 0.06635071 211 1.400447E-5 0.0111896
LSh.plSL2.50ch07V2 g 0.06635071 211 1.40045E-5 0.0111896
LSh.rlSL2.50ch07V1 g 0.06635071 211 1.400447E-5 0.0111896
LSh.rlSL2.50ch07V2 g 0.06635071 211 1.40045E-5 0.0111896
H.maxSL2.50ch08V1 g 0.07109005 211 6.344971E-8 0.0001013926
W.maxSL2.50ch02V1 g 0.1990521 211 4.303892E-7 0.000343881
W.maxSL2.50ch06V1 g 0.1682464 211 2.439171E-5 0.006496325
W.maxSL2.50ch11V2 t 0.4194313 211 1.145939E-6 0.0006104037
W.maxSL2.50ch11V4 g 0.3886256 211 9.652658E-8 0.0001542495
W.maxSL2.50ch11V8 c 0.3696682 211 5.61084E-6 0.00224153
W.maxSL2.50ch11V9 g 0.3767773 211 2.171462E-5 0.006496325
perSL2.50ch06V1 g 0.1682464 211 1.635761E-5 0.008886482
perSL2.50ch11V4 t 0.4194313 211 1.668301E-5 0.008886482
perSL2.50ch11V5 g 0.3886256 211 4.093177E-6 0.006540897
perSL2.50ch11V7 c 0.3696682 211 3.655515E-5 0.01302767
pan.macroSL2.50ch02V2 g 0.1990521 211 3.013045E-6 0.004814845
pan.macroSL2.50ch06V1 g 0.1682464 211 1.234299E-5 0.009862051
pan.microSL2.50ch04V1 c 0.08056872 211 2.87936E-5 0.04201133
piarSL2.50ch05V1 g 0.3933649 211 3.364496E-5 0.05376465
recSL2.50ch04V1 t 0.09004739 211 1.744638E-5 0.02787931
par.RSL2.50ch11V3 t 0.4194313 211 1.458645E-5 0.009301803
par.RSL2.50ch11V5 g 0.3886256 211 1.746271E-5 0.009301803
par.RSL2.50ch11V8 c 0.3696682 211 5.123873E-6 0.00818795
ptkSL2.50ch03V1 t 0.1066351 211 2.765348E-5 0.02265529
ptkSL2.50ch08V1 c 0.05924171 211 2.835456E-5 0.02265529
TNISL2.50ch02V1 g 0.1630435 184 2.710118E-6 0.004330768
verSL2.50ch11V3 g 0.3886256 211 7.987731E-6 0.01276439
verSL2.50ch11V6 c 0.3696682 211 2.669297E-5 0.02132768
W.midSL2.50ch02V2 g 0.1990521 211 5.681624E-7 0.0004539617
W.midSL2.50ch06V1 g 0.1682464 211 2.947811E-5 0.007851003
W.midSL2.50ch11V3 t 0.4194313 211 1.27744E-6 0.0006804499
W.midSL2.50ch11V4 g 0.3886256 211 1.044117E-7 0.0001668499
W.midSL2.50ch11V8 c 0.3696682 211 6.833154E-6 0.002729845
W.midSL2.50ch11V9 g 0.3767773 211 2.572145E-5 0.007851003
WwSL2.50ch08V1 g 0.07109005 211 2.917688E-5 0.04662466