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 mr1074 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
vg0222725881 sf0222720012 2 22725881 1.84E-37 1.52E-26
vg0224263868 sf0224257999 2 24263868 1.07E-11 NA
vg0224284988 sf0224279119 2 24284988 1.53E-10 NA
vg0224723224 sf0224717355 2 24723224 2.68E-10 3.84E-06
vg0221953494 sf0221947625 2 21953494 3.66E-10 1.33E-06
vg0224251301 sf0224245432 2 24251301 3.71E-09 1.21E-06
vg0225439704 sf0225433835 2 25439704 7.06E-09 7.42E-07
vg0223168818 sf0223162949 2 23168818 1.04E-08 1.89E-06
vg0224676560 sf0224670691 2 24676560 1.52E-08 8.62E-09
vg0222624829 sf0222618960 2 22624829 2.12E-08 6.07E-09
vg0222041029 sf0222035160 2 22041029 2.98E-08 3.55E-06
vg0222656032 sf0222650163 2 22656032 9.92E-08 7.98E-07
vg1112606022 sf1112142225 11 12606022 1.09E-07 9.61E-07
vg0224240409 sf0224234540 2 24240409 1.64E-07 3.12E-06
vg1215113033 sf1215110368 12 15113033 1.47E-06 NA
vg0710331865 sf0710330871 7 10331865 NA 4.27E-06