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 mr1651 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
vg0507954421 sf0507954362 5 7954421 6.30E-07 6.30E-07
vg1022845266 sf1022773739 10 22845266 1.71E-06 1.71E-06
vg0412792403 sf0412783113 4 12792403 1.95E-06 1.95E-06
vg1216138559 sf1216135855 12 16138559 2.09E-06 2.09E-06
vg0805425640 sf0805424643 8 5425640 2.36E-06 2.36E-06
vg0108533994 sf0108532994 1 8533994 2.38E-06 2.38E-06
vg0502517738 sf0502517714 5 2517738 2.39E-06 2.39E-06
vg1021675129 sf1021603607 10 21675129 2.45E-06 2.45E-06
vg0115090442 sf0115089416 1 15090442 3.10E-06 3.10E-06
vg0225238120 sf0225232251 2 25238120 3.22E-06 3.22E-06
vg0915249062 sf0915248061 9 15249062 4.02E-06 4.02E-06
vg0122974648 sf0122973604 1 22974648 4.05E-06 4.05E-06