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 mr1183 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 3.74E-25 3.86E-09
vg0222567385 sf0222561516 2 22567385 3.68E-23 1.00E-12
vg1009106434 sf1009035295 10 9106434 1.48E-22 NA
vg1104828509 sf1104824411 11 4828509 1.62E-19 NA
vg0425054754 sf0424869615 4 25054754 2.30E-19 NA
vg0104081958 sf0104080958 1 4081958 2.70E-19 NA
vg0222729853 sf0222723984 2 22729853 3.07E-18 5.01E-07
vg0407822984 sf0407818252 4 7822984 3.82E-18 2.43E-06
vg0222745198 sf0222739329 2 22745198 1.96E-17 5.52E-25
vg0222716080 sf0222710211 2 22716080 2.78E-17 1.37E-07
vg1009170616 sf1009099437 10 9170616 1.60E-16 1.50E-10
vg0317037608 sf0317036482 3 17037608 2.65E-15 1.18E-06
vg0528707749 sf0528645104 5 28707749 7.33E-15 3.18E-07
vg1006448469 sf1006464092 10 6448469 1.54E-14 5.00E-09
vg1007381584 sf1007397207 10 7381584 4.69E-13 8.02E-10
vg1120089078 sf1119623001 11 20089078 7.70E-13 1.27E-06
vg0223711747 sf0223705878 2 23711747 NA 1.06E-09
vg0209237133 sf0209237131 2 9237133 NA 7.28E-09
vg0224275719 sf0224269850 2 24275719 NA 4.38E-08
vg1217214923 sf1217208878 12 17214923 NA 2.00E-07
vg0410675332 sf0410666032 4 10675332 NA 3.92E-07
vg0222623646 sf0222617777 2 22623646 NA 1.08E-06
vg0223688129 sf0223682260 2 23688129 NA 1.31E-06
vg0809516128 sf0809515132 8 9516128 NA 2.96E-06
vg0600576478 sf0600575479 6 576478 NA 3.18E-06
vg0221650044 sf0221644175 2 21650044 NA 3.46E-06
vg0335804756 sf0335797625 3 35804756 NA 4.11E-06
vg0807842592 sf0807841596 8 7842592 NA 4.39E-06
vg1003606152 sf1003605129 10 3606152 NA 4.63E-06
vg0224480548 sf0224474679 2 24480548 NA 5.48E-06