GWAS Details

GWAS Basic Information

GWAS_ALCALAX_summer15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
3.83E-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 ALCALAX_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
ALCALAX_summer15 Asociación de Productores y Comercializadores de la Tomata de penjar d'Alcalá de Xivert field 1

Related GWAS Variants Summary 65

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
arSL2.50ch11V2 t 0.05607476635514 214 2.8666826910961E-7 0.00037352875464982
cirSL2.50ch10V1 t 0.08411214953271 214 2.6172985380045E-5 0.034103399950198
fse.curvedSL2.50ch02V2 g 0.08411214953271 214 2.004680028991E-5 0.013060490388876
fse.curvedSL2.50ch06V2 c 0.058411214953271 214 3.1073651822097E-6 0.0040488968324193
H.curvedSL2.50ch04V1 g 0.11682242990654 214 1.959761889087E-5 0.025535697414804
decSL2.50ch01V1 g 0.1098131 214 3.487964E-5 0.03987889
dblkSL2.50ch01V3 c 0.05140187 214 1.792698E-5 0.01373004
dblkSL2.50ch02V1 g 0.271028 214 2.107451E-5 0.01373004
desiSL2.50ch01V1 g 0.05140187 214 8.081368E-6 0.005265011
desiSL2.50ch01V2 c 0.05140187 214 2.09642E-7 0.0002731635
eaiSL2.50ch02V3 g 0.271028 214 2.619895E-5 0.03135883
FEC.orSL2.50ch07V1 g 0.07981221 213 2.591802E-6 0.003377118
FEC.pkSL2.50ch01V2 c 0.3802817 213 8.624506E-10 1.123773E-6
FEC.pkSL2.50ch08V2 c 0.06338028 213 3.300741E-5 0.02083397
FEC.rdSL2.50ch01V3 c 0.3802817 213 2.420253E-9 3.153589E-6
FEC.rdSL2.50ch01V5 g 0.1737089 213 5.316487E-6 0.001867386
FEC.rdSL2.50ch08V1 c 0.06338028 213 1.346448E-5 0.003508843
FEC.rdSL2.50ch08V2 g 0.06338028 213 4.428373E-6 0.001867386
FEC.rdSL2.50ch08V3 c 0.06338028 213 5.732573E-6 0.001867386
fec.bSL2.50ch01V1 c 0.3785047 214 2.262814E-5 0.02948446
FPS.lgSL2.50ch02V4 c 0.1173709 213 4.570049E-7 0.0002673455
FPS.lgSL2.50ch06V2 c 0.05868545 213 6.155307E-7 0.0002673455
FPS.lgSL2.50ch10V1 t 0.08450704 213 2.913319E-7 0.0002673455
FPS.ovoSL2.50ch03V1 c 0.08215962 213 4.348553E-9 5.666165E-6
FPS.oxSL2.50ch03V4 c 0.05399061 213 1.414887E-6 0.0006145326
FPS.oxSL2.50ch11V1 g 0.07981221 213 1.705931E-8 1.111414E-5
FPS.oxSL2.50ch11V2 g 0.07042254 213 6.85703E-9 8.934711E-6
fasSL2.50ch01V1 g 0.05868545 213 1.780794E-5 0.01160188
fasSL2.50ch11V10 c 0.08450704 213 2.90293E-6 0.003782517
fse.ISL2.50ch02V3 g 0.08411215 214 2.570848E-5 0.01674907
fse.ISL2.50ch06V2 c 0.05841121 214 4.22349E-6 0.005503208
fse.IISL2.50ch06V2 c 0.05841121 214 6.013981E-6 0.007836217
fsiSL2.50ch06V2 c 0.05841121 214 9.115842E-6 0.01187794
triSL2.50ch01V1 c 0.0817757 214 1.500489E-5 0.009775683
triSL2.50ch01V2 g 0.1074766 214 2.811461E-5 0.01221111
triSL2.50ch02V1 a 0.06775701 214 1.462253E-5 0.009775683
FWSL2.50ch11V5 t 0.05607477 214 3.571722E-5 0.02326977
FWSL2.50ch11V13 c 0.08411215 214 2.895778E-6 0.003773198
jpSL2.50ch03V1 g 0.1197183 213 5.359865E-6 0.003491952
jpSL2.50ch04V1 c 0.1830986 213 1.291253E-5 0.005608342
jpSL2.50ch11V19 g 0.07276995 213 8.543704E-8 0.0001113245
lcnSL2.50ch11V10 g 0.0771028 214 1.262366E-5 0.008224316
lcnSL2.50ch11V14 c 0.08411215 214 8.908616E-9 1.160793E-5
lcnSL2.50ch12V19 c 0.4883178 214 3.710266E-5 0.01611492
LSh.plSL2.50ch03V1 a 0.1103286 213 3.148531E-5 0.04102536
LSh.rlSL2.50ch03V1 a 0.1103286 213 3.148531E-5 0.04102536
H.maxSL2.50ch04V1 g 0.1168224 214 3.392512E-5 0.04420443
perSL2.50ch11V2 t 0.05607477 214 8.44333E-7 0.001100166
pan.microSL2.50ch06V1 c 0.05841121 214 1.09655E-5 0.01428804
pblkSL2.50ch01V1 g 0.05140187 214 1.44045E-5 0.01876906
recSL2.50ch01V1 g 0.05140187 214 3.528947E-5 0.01194963
recSL2.50ch01V2 c 0.05140187 214 8.220776E-6 0.005355836
recSL2.50ch01V3 g 0.05140187 214 3.668344E-5 0.01194963
recSL2.50ch02V1 g 0.271028 214 2.662053E-6 0.003468656
SkCSL2.50ch01V3 c 0.3802817 213 7.548102E-9 9.835177E-6
SkCSL2.50ch01V5 g 0.1737089 213 3.514418E-5 0.02104344
SPS.dtSL2.50ch01V1 a 0.05424528 212 1.303452E-6 0.001698397
SPS.stSL2.50ch01V1 a 0.05424528 212 1.303452E-6 0.001698397
par.RSL2.50ch11V7 c 0.08411215 214 4.39573E-6 0.005727636
ptk.RSL2.50ch08V1 c 0.1051402 214 1.887486E-5 0.008055445
ptk.RSL2.50ch08V2 g 0.07943925 214 1.230478E-5 0.008016564
ptk.RSL2.50ch08V3 g 0.05140187 214 1.37539E-6 0.001792133
ptk.RSL2.50ch08V4 a 0.0817757 214 2.472892E-5 0.008055445
verSL2.50ch11V2 t 0.05607477 214 2.707519E-5 0.01763948
verSL2.50ch11V5 c 0.08411215 214 8.393552E-6 0.0109368