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 mr1193 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
vg0225285799 sf0225279930 2 25285799 3.09E-08 3.09E-08
vg0420812162 sf0420640205 4 20812162 2.05E-07 2.05E-07
vg0142370628 sf0142369584 1 42370628 7.02E-07 7.02E-07
vg1218458718 sf1218430154 12 18458718 1.71E-06 1.71E-06
vg0604702911 sf0604701912 6 4702911 2.23E-06 2.23E-06
vg0115241228 sf0115240202 1 15241228 2.59E-06 2.59E-06
vg0719611742 sf0719610749 7 19611742 2.59E-06 2.59E-06
vg0118445194 sf0118444148 1 18445194 4.03E-06 4.03E-06