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 mr1781 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
vg0427271689 sf0427086558 4 27271689 2.92E-06 2.92E-06
vg0820990102 sf0820987389 8 20990102 3.50E-06 3.50E-06
vg0628126153 sf0628125155 6 28126153 4.28E-06 4.28E-06
vg1109530315 sf1109524892 11 9530315 4.91E-06 4.91E-06
vg0909181183 sf0909180182 9 9181183 5.09E-06 5.09E-06