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 mr1477 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
vg0726232859 sf0726231865 7 26232859 9.47E-09 NA
vg0602861181 sf0602860182 6 2861181 2.81E-08 1.06E-06
vg0435288012 sf0435102893 4 35288012 2.93E-08 4.17E-06
vg0123683620 sf0123682576 1 23683620 3.30E-08 NA
vg1124448492 sf1123982332 11 24448492 7.23E-08 NA
vg0225476794 sf0225470925 2 25476794 1.34E-06 4.47E-06
vg0315246943 sf0315245590 3 15246943 2.51E-06 NA
vg0225538225 sf0225532356 2 25538225 4.45E-06 NA
vg0721855491 sf0721854498 7 21855491 7.50E-06 NA
vg1004566717 sf1004583255 10 4566717 8.18E-06 3.84E-06
vg1117245312 sf1116779164 11 17245312 NA 2.45E-06
vg0335609936 sf0335602805 3 35609936 NA 5.79E-06