GWAS Details

GWAS Basic Information

GWAS_ACTYMPAKY_autumn15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
2.46E-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 ACTYMPAKY_autumn15. 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
ACTYMPAKY_autumn15 Agrotobiomchanikos Synetairismos Tympakioy

Related GWAS Variants Summary 51

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
fic.aSL2.50ch10V1 G 0.064102564102564 117 2.6277278571202E-5 0.053316598220969
fic.greenSL2.50ch08V1 c 0.14102564102564 117 1.4222306850811E-5 0.024946040324122
fic.greenSL2.50ch08V2 g 0.13675213675214 117 3.6230308031815E-5 0.024946040324122
fic.greenSL2.50ch11V1 g 0.076923076923077 117 3.6884239020388E-5 0.024946040324122
fic.HSL2.50ch10V1 G 0.064102564102564 117 1.9940114171621E-5 0.039160117333932
fic.LSL2.50ch08V1 c 0.1410256 117 2.70442E-5 0.04730754
fic.lumSL2.50ch07V1 G 0.05128205 117 3.480624E-5 0.06410347
FEC.pkSL2.50ch01V3 c 0.1016949 118 7.082541E-9 1.437048E-5
FEC.rdSL2.50ch01V4 c 0.1016949 118 2.889576E-7 0.000586295
FEC.ylSL2.50ch06V1 c 0.08050847 118 6.712174E-6 0.003120193
FEC.ylSL2.50ch08V1 t 0.08050847 118 2.951627E-5 0.007486064
FEC.ylSL2.50ch08V2 a 0.07627119 118 2.33652E-5 0.006772571
FEC.ylSL2.50ch08V3 c 0.06355932 118 3.644372E-6 0.003120193
FEC.ylSL2.50ch08V4 c 0.1398305 118 6.455943E-6 0.003120193
FEC.ylSL2.50ch08V5 g 0.1355932 118 1.483781E-5 0.005017652
FEC.ylSL2.50ch10V1 g 0.06355932 118 1.861289E-7 0.0003776556
FEC.ylSL2.50ch11V1 g 0.08050847 118 7.688991E-6 0.003120193
ellSL2.50ch05V1 g 0.1100917 109 3.562881E-5 0.07229086
fec.aSL2.50ch10V1 g 0.06315789 95 2.430227E-5 0.04930931
FPS.HtSL2.50ch06V1 a 0.05752212 113 1.451964E-5 0.009820115
FPS.HtSL2.50ch08V9 g 0.05752212 113 5.212341E-6 0.00528792
FPS.HtSL2.50ch12V1 c 0.05752212 113 1.480907E-6 0.003004761
FPS.ovoSL2.50ch01V1 t 0.05309735 113 2.705877E-7 0.0005490224
FPS.ovoSL2.50ch05V1 t 0.07964602 113 2.678888E-5 0.01358866
FPS.ovoSL2.50ch06V1 a 0.05752212 113 6.982612E-6 0.004850119
FPS.ovoSL2.50ch08V2 c 0.05752212 113 7.171196E-6 0.004850119
FPS.recSL2.50ch12V1 c 0.0619469 113 2.624511E-8 5.325133E-5
FPS.rdSL2.50ch01V1 a 0.04867257 113 5.130761E-6 0.01041031
fse.ISL2.50ch02V2 g 0.293578 109 7.77436E-6 0.01577418
fse.IISL2.50ch02V2 g 0.293578 109 8.178306E-6 0.01659378
fsiSL2.50ch02V2 g 0.293578 109 8.209441E-6 0.01665696
FShSSL2.50ch02V4 g 0.3103448 116 5.858697E-6 0.0118873
FWSL2.50ch11V8 g 0.3473684 95 3.745349E-6 0.007599313
GHSL2.50ch08V1 c 0.05508475 118 1.775185E-5 0.0360185
Hu1ISL2.50ch00V1 a 0.4913793 116 2.65983E-5 0.04308772
jpSL2.50ch03V2 c 0.05555556 117 1.427301E-5 0.002804925
jpSL2.50ch05V1 t 0.05128205 117 9.587944E-7 0.0004863485
jpSL2.50ch05V4 c 0.05128205 117 4.545537E-6 0.001537149
jpSL2.50ch05V9 g 0.05128205 117 1.520659E-5 0.002804925
jpSL2.50ch05V10 t 0.05128205 117 1.159659E-5 0.002614387
jpSL2.50ch09V3 a 0.05555556 117 6.297317E-6 0.001825322
jpSL2.50ch09V4 t 0.05555556 117 4.42488E-6 0.001537149
jpSL2.50ch11V9 c 0.05982906 117 1.030369E-5 0.002613273
jpSL2.50ch11V16 c 0.05555556 117 2.538928E-8 5.151486E-5
jpSL2.50ch11V20 g 0.08547009 117 5.354918E-7 0.0003621709
jpSL2.50ch11V21 a 0.08119658 117 4.107154E-7 0.0003621709
lcnSL2.50ch11V9 g 0.3577586 116 1.763737E-7 0.0003578622
lcnSL2.50ch11V16 c 0.387931 116 3.831177E-6 0.003886729
RCESL2.50ch11V8 c 0.3938053 113 2.984808E-5 0.06056175
SkCSL2.50ch01V2 c 0.1016949 118 7.082541E-9 1.437048E-5
WwSL2.50ch04V1 c 0.04587156 109 9.296391E-6 0.01886238