Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1503 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0222725003 sf0222719134 2 22725003 7.92E-27 6.68E-10
vg1009106434 sf1009035295 10 9106434 1.62E-23 NA
vg0222567385 sf0222561516 2 22567385 3.91E-23 3.40E-13
vg1104828509 sf1104824411 11 4828509 4.70E-20 NA
vg0425054754 sf0424869615 4 25054754 1.55E-19 NA
vg0104081958 sf0104080958 1 4081958 3.63E-19 NA
vg0222735698 sf0222729829 2 22735698 1.19E-18 8.65E-25
vg0222729853 sf0222723984 2 22729853 1.23E-18 2.36E-07
vg1008002204 sf1008042033 10 8002204 4.08E-17 3.11E-10
vg1009170616 sf1009099437 10 9170616 1.43E-16 1.07E-11
vg1006696551 sf1006712174 10 6696551 2.42E-16 1.00E-06
vg0528707471 sf0528644826 5 28707471 7.61E-15 1.29E-07
vg1006448469 sf1006464092 10 6448469 2.97E-14 3.06E-09
vg0223711747 sf0223705878 2 23711747 NA 2.32E-09
vg0223688130 sf0223682261 2 23688130 NA 4.59E-09
vg0209237133 sf0209237131 2 9237133 NA 3.36E-08
vg0224275719 sf0224269850 2 24275719 NA 1.99E-07
vg0410675332 sf0410666032 4 10675332 NA 3.94E-07
vg0807842592 sf0807841596 8 7842592 NA 7.34E-07
vg1214403070 sf1214400411 12 14403070 NA 9.47E-07
vg1217214923 sf1217208878 12 17214923 NA 1.00E-06
vg0222637418 sf0222631549 2 22637418 NA 1.14E-06
vg1007540239 sf1007555851 10 7540239 NA 1.35E-06
vg0809871555 sf0809870559 8 9871555 NA 1.59E-06
vg0221650044 sf0221644175 2 21650044 NA 1.70E-06
vg0600576478 sf0600575479 6 576478 NA 2.18E-06
vg1120089078 sf1119623001 11 20089078 NA 2.68E-06
vg0812069180 sf0812068185 8 12069180 NA 3.78E-06
vg0224286805 sf0224280936 2 24286805 NA 4.78E-06
vg0224480548 sf0224474679 2 24480548 NA 5.43E-06