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 mr1402 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
vg0222719538 sf0222713669 2 22719538 9.01E-13 1.49E-08
vg0223170193 sf0223164324 2 23170193 3.01E-09 NA
vg0618618072 sf0618617075 6 18618072 3.29E-09 1.03E-06
vg0707711778 sf0707710783 7 7711778 6.80E-09 1.28E-06
vg0617779892 sf0617778895 6 17779892 1.89E-08 NA
vg0707896183 sf0707895188 7 7896183 1.06E-06 NA
vg0412175929 sf0412166640 4 12175929 1.44E-06 3.94E-06
vg1124078478 sf1123612348 11 24078478 7.70E-06 2.77E-06
vg0600116582 sf0600115582 6 116582 NA 2.63E-06