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 mr1970 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
vg0607383997 sf0607382998 6 7383997 1.31E-21 1.13E-11
vg0607467410 sf0607466411 6 7467410 4.20E-21 2.62E-13
vg0606974869 sf0606973870 6 6974869 1.81E-12 1.16E-08
vg1117508504 sf1117042359 11 17508504 1.69E-11 NA
vg0721227076 sf0721226083 7 21227076 2.76E-11 NA
vg0429319185 sf0429134051 4 29319185 1.66E-10 NA
vg0334583436 sf0334576306 3 34583436 5.73E-09 4.23E-06
vg0706567685 sf0706566690 7 6567685 5.09E-07 5.86E-07
vg0107527372 sf0107526372 1 7527372 NA 3.97E-06
vg0603271543 sf0603270544 6 3271543 NA 7.90E-06