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
vg0128529554 sf0128528509 1 28529554 7.97E-13 NA
vg0123696378 sf0123695334 1 23696378 8.00E-12 NA
vg1104988610 sf1104984421 11 4988610 1.96E-11 NA
vg0821751104 sf0821748391 8 21751104 5.01E-11 NA
vg0131535738 sf0131534694 1 31535738 5.20E-11 NA
vg1116933718 sf1116468597 11 16933718 7.93E-10 6.91E-06
vg1018654736 sf1018583294 10 18654736 2.62E-09 2.97E-06