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 mr1888 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
vg1101745249 sf1101744250 11 1745249 5.37E-41 NA
vg0406401975 sf0406397415 4 6401975 6.17E-41 2.14E-08
vg0520914961 sf0520852402 5 20914961 1.42E-40 NA
vg1116956482 sf1116491359 11 16956482 3.42E-40 NA
vg0406420728 sf0406416168 4 6420728 3.94E-40 7.47E-09
vg0716998436 sf0716997443 7 16998436 5.08E-40 NA
vg0406399726 sf0406395166 4 6399726 1.39E-38 1.25E-08
vg0518677933 sf0518615416 5 18677933 1.15E-37 NA
vg0729357717 sf0729356725 7 29357717 4.96E-37 4.11E-06
vg0808439427 sf0808438431 8 8439427 NA 8.86E-07
vg0505756122 sf0505756060 5 5756122 NA 5.93E-06
vg1209878818 sf1209876228 12 9878818 NA 6.24E-06
vg1126519704 sf1126048119 11 26519704 NA 6.32E-06
vg0229707033 sf0229701164 2 29707033 NA 8.99E-06