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 mr1902 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
vg0331247251 sf0331240136 3 31247251 2.26E-20 1.52E-09
vg0331248975 sf0331241860 3 31248975 2.67E-20 5.27E-11
vg1119716424 sf1119250112 11 19716424 6.59E-14 NA
vg1116217816 sf1115752686 11 16217816 2.16E-13 NA
vg1113429006 sf1112965328 11 13429006 3.13E-12 8.39E-06
vg1109129387 sf1109123966 11 9129387 9.77E-12 NA
vg0314568077 sf0314566764 3 14568077 2.66E-11 3.08E-06
vg0314533547 sf0314532235 3 14533547 1.52E-09 7.89E-06
vg1126950755 sf1126479142 11 26950755 NA 2.32E-06
vg0327794881 sf0327787935 3 27794881 NA 3.66E-06