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 mr1631 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
vg0405488386 sf0405483827 4 5488386 1.58E-08 7.04E-08
vg0427650738 sf0427465601 4 27650738 1.96E-08 1.95E-06
vg0427367311 sf0427182175 4 27367311 2.08E-08 1.61E-06
vg0322360535 sf0322359024 3 22360535 9.72E-07 7.48E-06
vg1126117503 sf1125645917 11 26117503 4.40E-06 6.17E-06
vg0406265720 sf0406261160 4 6265720 6.43E-06 3.53E-06
vg0907678745 sf0907677745 9 7678745 6.43E-06 4.32E-06
vg0225356942 sf0225351073 2 25356942 8.28E-06 NA