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 mr1966 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
vg0424824884 sf0424639745 4 24824884 1.33E-11 NA
vg0919306527 sf0919306117 9 19306527 3.33E-11 NA
vg0726312270 sf0726311276 7 26312270 4.77E-11 NA
vg0220368674 sf0220362806 2 20368674 1.02E-10 NA
vg0304248883 sf0304247885 3 4248883 2.93E-10 NA
vg1117554106 sf1117087962 11 17554106 3.79E-07 NA
vg0705219291 sf0705218292 7 5219291 1.55E-06 NA
vg1215690354 sf1215687651 12 15690354 NA 5.28E-07
vg0805022482 sf0805021485 8 5022482 NA 4.05E-06