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 mr1992 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
vg1218087139 sf1218058575 12 18087139 4.75E-09 8.08E-06
vg0314748691 sf0314747378 3 14748691 9.57E-09 1.15E-06
vg1218365153 sf1218336589 12 18365153 1.76E-08 3.74E-06
vg0521967774 sf0521905216 5 21967774 8.07E-08 NA
vg0314727170 sf0314725857 3 14727170 4.30E-06 3.43E-06
vg0522018946 sf0521956388 5 22018946 NA 7.39E-07
vg0314967098 sf0314965745 3 14967098 NA 2.28E-06