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 mr1522 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
vg0307871179 sf0307870117 3 7871179 1.23E-17 NA
vg0205737867 sf0205737867 2 5737867 3.93E-17 NA
vg1109566448 sf1109561025 11 9566448 1.54E-16 NA
vg0616753926 sf0616752928 6 16753926 1.93E-16 NA
vg0718862748 sf0718861755 7 18862748 3.71E-16 NA
vg0401290717 sf0401286267 4 1290717 6.08E-13 NA
vg0324882835 sf0324880914 3 24882835 NA 2.68E-06
vg0630508777 sf0630507779 6 30508777 NA 3.59E-06