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 mr1720 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
vg0141992653 sf0141991610 1 41992653 1.54E-09 3.13E-06
vg1124829861 sf1124363701 11 24829861 2.69E-09 NA
vg1100923864 sf1100922865 11 923864 4.43E-09 2.36E-06
vg0327983003 sf0327976057 3 27983003 4.90E-09 NA
vg1119968697 sf1119502620 11 19968697 8.41E-09 NA
vg0728077698 sf0728076705 7 28077698 2.32E-08 NA
vg0404527989 sf0404523592 4 4527989 7.77E-08 1.49E-07
vg0129861515 sf0129860470 1 29861515 5.72E-07 1.10E-06
vg1011434213 sf1011363032 10 11434213 1.25E-06 2.11E-06
vg0306688786 sf0306687786 3 6688786 3.15E-06 6.51E-07
vg1008686103 sf1008614965 10 8686103 NA 3.88E-06
vg0216120581 sf0216114711 2 16120581 NA 4.89E-06