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 mr1808 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
vg1103963461 sf1103959363 11 3963461 1.97E-06 1.97E-06
vg0914238396 sf0914237395 9 14238396 2.20E-06 2.20E-06
vg0308057027 sf0308055965 3 8057027 2.35E-06 2.35E-06
vg0617763556 sf0617762559 6 17763556 2.40E-06 2.40E-06
vg0922557712 sf0922557231 9 22557712 2.91E-06 2.91E-06
vg1103973230 sf1103969132 11 3973230 3.12E-06 3.12E-06
vg1200334317 sf1200333317 12 334317 4.66E-06 4.66E-06
vg0617795766 sf0617794769 6 17795766 6.53E-06 6.53E-06