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 mr1623 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
vg0818658445 sf0818655732 8 18658445 3.88E-07 3.88E-07
vg1010745933 sf1010674754 10 10745933 4.35E-07 4.35E-07
vg0521737035 sf0521674477 5 21737035 5.00E-07 5.00E-07
vg0917631772 sf0917630771 9 17631772 6.79E-07 6.79E-07
vg1219878412 sf1219849882 12 19878412 1.36E-06 1.37E-06
vg0911104766 sf0911103765 9 11104766 1.89E-06 1.89E-06
vg0529385032 sf0529322387 5 29385032 2.74E-06 2.74E-06
vg1209054055 sf1209051464 12 9054055 2.96E-06 2.96E-06
vg1117720843 sf1117254699 11 17720843 4.11E-06 4.11E-06
vg0921058093 sf0921057612 9 21058093 4.25E-06 4.25E-06