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 mr1930 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
vg0819535183 sf0819532470 8 19535183 1.54E-08 3.47E-06
vg0209213036 sf0209213034 2 9213036 3.18E-06 2.27E-06
vg0821071524 sf0821068811 8 21071524 NA 4.53E-07
vg0316269128 sf0316267775 3 16269128 NA 2.00E-06
vg1219759455 sf1219730925 12 19759455 NA 2.42E-06
vg1219758962 sf1219730432 12 19758962 NA 2.68E-06