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 mr1735 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
vg0726945885 sf0726944891 7 26945885 1.67E-12 6.15E-06
vg0726837546 sf0726836552 7 26837546 7.10E-11 4.38E-06
vg0724004854 sf0724003860 7 24004854 2.60E-10 4.77E-07
vg0130452125 sf0130451081 1 30452125 2.17E-09 NA
vg1104979071 sf1104974882 11 4979071 3.72E-09 NA
vg1102430558 sf1102426462 11 2430558 7.10E-09 NA
vg1217993198 sf1217964634 12 17993198 7.39E-09 3.69E-06