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 mr1992 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
vg0525796139 sf0525733560 5 25796139 7.73E-07 7.74E-07
vg0527911923 sf0527849280 5 27911923 1.65E-06 1.65E-06
vg0805826839 sf0805825842 8 5826839 2.15E-06 2.15E-06
vg0300375981 sf0300374979 3 375981 2.36E-06 2.36E-06
vg0701005739 sf0701004739 7 1005739 2.53E-06 2.53E-06
vg0527942741 sf0527880097 5 27942741 3.18E-06 3.18E-06
vg1103160536 sf1103156439 11 3160536 3.56E-06 3.57E-06