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 mr1382 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
vg0825549651 sf0825546937 8 25549651 3.67E-09 NA
vg0825058570 sf0825055856 8 25058570 1.74E-08 NA
vg0827703459 sf0827700745 8 27703459 2.90E-08 NA
vg0126646322 sf0126645278 1 26646322 5.20E-08 NA
vg1110030990 sf1110025567 11 10030990 9.00E-08 NA
vg0210599980 sf0210599978 2 10599980 2.75E-07 8.00E-06
vg0721904261 sf0721903268 7 21904261 4.26E-07 NA
vg0821794641 sf0821791928 8 21794641 2.25E-06 NA
vg1126198147 sf1125726561 11 26198147 9.33E-06 NA
vg0314706879 sf0314705566 3 14706879 NA 1.03E-06