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 mr1984 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
vg0805992743 sf0805991746 8 5992743 4.64E-07 4.64E-07
vg0915815139 sf0915814138 9 15815139 2.19E-06 2.19E-06
vg1117099077 sf1116632929 11 17099077 2.38E-06 2.38E-06
vg0223522948 sf0223517079 2 23522948 2.76E-06 2.76E-06
vg0138706549 sf0138705506 1 38706549 2.96E-06 2.96E-06
vg0134670870 sf0134669827 1 34670870 3.87E-06 3.87E-06
vg0142427760 sf0142426716 1 42427760 4.97E-06 4.97E-06
vg0223518528 sf0223512659 2 23518528 8.34E-06 8.34E-06