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 mr1359 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
vg0431858725 sf0431673619 4 31858725 1.19E-10 NA
vg1217403317 sf1217397272 12 17403317 2.35E-10 NA
vg1117746722 sf1117280578 11 17746722 2.77E-10 NA
vg1207825767 sf1207823173 12 7825767 3.05E-10 NA
vg0131782297 sf0131781253 1 31782297 5.19E-10 NA
vg1118097592 sf1117631450 11 18097592 1.32E-08 NA
vg1116933705 sf1116468584 11 16933705 NA 3.70E-06