GWAS Details

GWAS Basic Information

GWAS_GARBI1_summer15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
3.42E-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 GARBI1_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
GARBI1_summer15 Progrés Garbí

Related GWAS Variants Summary 33

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
fse.curvedSL2.50ch00V3 c 0.048 125 3.6720131062469E-7 0.00053574671220143
fse.curvedSL2.50ch06V1 c 0.1 125 1.8132123306411E-6 0.0013227383952027
fse.curvedSL2.50ch08V2 g 0.064 125 1.9519547146002E-5 0.0094930064286725
dan.macroSL2.50ch08V2 c 0.376 125 6.7183956298443E-6 0.0098021392239428
FPS.HtSL2.50ch02V1 c 0.0625 128 1.7353415092433E-5 0.0042197721033101
FPS.HtSL2.50ch02V2 c 0.0625 128 1.7353415092433E-5 0.0042197721033101
FPS.HtSL2.50ch02V3 g 0.04296875 128 5.865244397281E-9 2.8524638585443E-6
FPS.HtSL2.50ch08V1 g 0.0703125 128 1.0749664583512E-9 7.8418803136721E-7
FPS.HtSL2.50ch08V4 g 0.0625 128 3.4872339599179E-7 0.000127196858688
FPS.HtSL2.50ch08V6 t 0.07421875 128 3.4016589680466E-10 4.96302043438E-7
FPS.lgSL2.50ch00V4 c 0.046875 128 5.2600088367352E-6 0.0025581176309322
FPS.lgSL2.50ch02V2 g 0.0625 128 8.6182762204585E-6 0.0031435162514122
FPS.lgSL2.50ch02V5 c 0.08203125 128 1.6055958532535E-5 0.0046851286997937
FPS.lgSL2.50ch06V1 c 0.09765625 128 5.916640752495E-7 0.00055586055548799
FPS.lgSL2.50ch08V2 g 0.0625 128 7.6197471622754E-7 0.00055586055548799
FPS.ovoSL2.50ch09V1 a 0.05078125 128 1.7373216596816E-5 0.025347523014754
fse.ISL2.50ch00V3 c 0.048 125 2.704255E-7 0.0003945508
fse.ISL2.50ch06V1 c 0.1 125 2.884697E-6 0.002104387
fse.ISL2.50ch08V4 g 0.064 125 2.938186E-5 0.01071703
fse.ISL2.50ch08V5 c 0.376 125 2.372706E-5 0.01071703
fse.IISL2.50ch00V3 c 0.048 125 5.322304E-7 0.0007765241
fse.IISL2.50ch06V1 c 0.1 125 3.28689E-6 0.002397786
fse.IISL2.50ch08V3 g 0.064 125 3.553929E-5 0.01296296
fse.IISL2.50ch08V4 c 0.376 125 2.777886E-5 0.01296296
fsiSL2.50ch00V3 c 0.048 125 5.251195E-7 0.0007661493
fsiSL2.50ch06V1 c 0.1 125 3.222716E-6 0.002350972
fsiSL2.50ch08V3 g 0.064 125 3.680288E-5 0.01342385
fsiSL2.50ch08V4 c 0.376 125 2.763381E-5 0.01342385
jpSL2.50ch00V6 c 0.05223881 134 6.542368E-6 0.009545315
LSh.dfSL2.50ch02V1 t 0.07777778 135 2.978123E-5 0.01881874
LSh.dfSL2.50ch08V1 c 0.08518519 135 2.146429E-5 0.01881874
SPS.lnSL2.50ch10V1 g 0.06666667 135 2.089499E-7 0.0003048579
ptkSL2.50ch10V1 a 0.052 125 3.57541E-5 0.05216523