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 mr1053 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
vg1009167787 sf1009096608 10 9167787 1.51E-12 1.86E-08
vg0315306356 sf0315305003 3 15306356 6.76E-12 NA
vg0412457585 sf0412448300 4 12457585 7.59E-12 5.85E-08
vg1117469579 sf1117003434 11 17469579 7.33E-11 NA
vg0714251445 sf0714250452 7 14251445 7.47E-11 5.70E-07
vg0813556857 sf0813554410 8 13556857 4.64E-10 2.10E-06
vg0714251796 sf0714250803 7 14251796 6.08E-10 4.52E-07
vg0905695815 sf0905694815 9 5695815 7.53E-10 NA
vg1121617785 sf1121151662 11 21617785 5.25E-09 5.87E-07
vg0719045974 sf0719044981 7 19045974 2.60E-07 4.19E-06
vg0628246864 sf0628245866 6 28246864 3.57E-07 2.72E-06
vg1009502056 sf1009430877 10 9502056 NA 2.32E-07
vg1009644609 sf1009573430 10 9644609 NA 1.27E-06
vg0819114790 sf0819112077 8 19114790 NA 1.46E-06
vg0230183930 sf0230178061 2 30183930 NA 9.72E-06