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 mr1659 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
vg0623198034 sf0623197037 6 23198034 8.45E-13 1.79E-09
vg1215769622 sf1215766919 12 15769622 6.82E-09 3.47E-06
vg0321403368 sf0321401878 3 21403368 1.21E-08 NA
vg0321406609 sf0321405119 3 21406609 2.62E-08 3.39E-06
vg1215556442 sf1215553739 12 15556442 5.37E-08 4.12E-07
vg1215673774 sf1215671071 12 15673774 2.47E-07 NA