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 mr1810 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
vg1218087170 sf1218058606 12 18087170 1.13E-11 1.23E-06
vg0133079922 sf0133078878 1 33079922 3.58E-10 NA
vg0328102119 sf0328095173 3 28102119 5.61E-10 NA
vg0619349707 sf0619348710 6 19349707 7.99E-10 NA
vg0916428508 sf0916427507 9 16428508 1.22E-09 NA
vg0910450391 sf0910449390 9 10450391 1.29E-09 4.87E-06