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 mr1605 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
vg0431515534 sf0431330433 4 31515534 2.50E-07 2.51E-07
vg0118269761 sf0118268715 1 18269761 1.02E-06 1.02E-06
vg1214822308 sf1214819649 12 14822308 1.32E-06 1.32E-06
vg0905354568 sf0905353568 9 5354568 1.37E-06 1.37E-06
vg1214134657 sf1214131997 12 14134657 1.38E-06 1.38E-06
vg0914989973 sf0914988972 9 14989973 2.20E-06 2.20E-06
vg1207090120 sf1207089010 12 7090120 2.41E-06 2.41E-06
vg0431750098 sf0431564990 4 31750098 4.94E-06 4.94E-06