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 mr1376 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
vg0125460621 sf0125459577 1 25460621 6.73E-11 9.15E-06
vg0123690615 sf0123689571 1 23690615 1.49E-09 NA
vg0128497255 sf0128496210 1 28497255 1.63E-09 NA
vg1104979071 sf1104974882 11 4979071 3.55E-09 NA
vg0710432728 sf0710431734 7 10432728 2.59E-08 NA
vg0431655631 sf0431470524 4 31655631 3.38E-08 1.17E-06
vg0431614108 sf0431429003 4 31614108 3.42E-08 4.07E-06
vg0726849875 sf0726848881 7 26849875 6.20E-08 NA
vg1015779989 sf1015708759 10 15779989 1.19E-06 NA
vg1106375766 sf1106371518 11 6375766 3.17E-06 1.58E-06
vg1116933718 sf1116468597 11 16933718 3.34E-06 4.89E-06
vg1109530380 sf1109524957 11 9530380 NA 3.64E-06