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 mr1031 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
vg1208105826 sf1208103232 12 8105826 6.57E-22 2.71E-06
vg1208659303 sf1208656710 12 8659303 5.09E-21 7.65E-07
vg0433930554 sf0433745450 4 33930554 7.15E-21 1.04E-11
vg0529082765 sf0529020120 5 29082765 1.66E-20 8.36E-06
vg1214071883 sf1214069223 12 14071883 8.75E-20 NA
vg0228684554 sf0228678685 2 28684554 1.90E-19 NA
vg0130113615 sf0130112570 1 30113615 1.25E-17 8.04E-06
vg0122562214 sf0122561169 1 22562214 3.32E-16 2.45E-06
vg1208553492 sf1208550899 12 8553492 8.82E-16 2.80E-06
vg0905473217 sf0905472217 9 5473217 NA 3.43E-06