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 mr1102 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
vg0318764893 sf0318763653 3 18764893 7.30E-07 7.30E-07
vg1115442463 sf1114978775 11 15442463 1.04E-06 1.05E-06
vg1109206941 sf1109201520 11 9206941 2.05E-06 2.05E-06
vg0507827115 sf0507827056 5 7827115 3.00E-06 3.00E-06
vg0323047220 sf0323045708 3 23047220 3.37E-06 3.37E-06
vg0209816315 sf0209816313 2 9816315 3.85E-06 3.85E-06
vg0602906214 sf0602905215 6 2906214 3.86E-06 3.86E-06
vg0319023309 sf0319022069 3 19023309 3.97E-06 3.97E-06
vg1110660768 sf1110655313 11 10660768 4.31E-06 4.31E-06