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 mr1096 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
vg0610648813 sf0610647814 6 10648813 1.26E-15 4.71E-12
vg0610752378 sf0610751379 6 10752378 9.43E-15 1.88E-12
vg0610059822 sf0610058823 6 10059822 1.30E-10 2.06E-09
vg0403922278 sf0403917884 4 3922278 5.62E-10 3.89E-07
vg0610435197 sf0610434198 6 10435197 1.93E-09 1.71E-07
vg1225125551 sf1225092005 12 25125551 1.99E-09 NA
vg0122531612 sf0122530567 1 22531612 2.69E-09 NA
vg0626895745 sf0626894748 6 26895745 2.77E-09 4.36E-07
vg0139829148 sf0139828105 1 39829148 5.04E-08 4.68E-06
vg0506178976 sf0506178915 5 6178976 2.05E-06 NA