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 mr1752 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
vg0431515534 sf0431330433 4 31515534 1.91E-07 1.92E-07
vg1215167085 sf1215164421 12 15167085 6.77E-07 6.78E-07
vg0428458707 sf0428273560 4 28458707 7.02E-07 7.04E-07
vg0719159480 sf0719158487 7 19159480 1.40E-06 1.40E-06
vg0300265158 sf0300264158 3 265158 1.89E-06 1.90E-06
vg0203000556 sf0203000554 2 3000556 2.41E-06 2.40E-06
vg0218624032 sf0218618163 2 18624032 2.61E-06 2.62E-06
vg0805546679 sf0805545682 8 5546679 3.64E-06 3.65E-06
vg1214134657 sf1214131997 12 14134657 3.87E-06 3.88E-06
vg0819535046 sf0819532333 8 19535046 4.51E-06 4.52E-06
vg0320043666 sf0320042177 3 20043666 4.74E-06 4.75E-06