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 mr1996 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
vg0123673583 sf0123672539 1 23673583 3.28E-12 9.64E-06
vg0307000761 sf0306999759 3 7000761 4.92E-12 NA
vg0123578067 sf0123577023 1 23578067 1.51E-11 3.58E-06
vg0223849476 sf0223843607 2 23849476 4.28E-11 NA
vg0137111389 sf0137110346 1 37111389 8.26E-11 NA
vg1126520429 sf1126048844 11 26520429 8.46E-11 NA
vg0715703024 sf0715702031 7 15703024 6.71E-10 1.97E-06
vg1126542743 sf1126071158 11 26542743 1.81E-09 6.11E-09
vg1127020065 sf1126548452 11 27020065 9.94E-07 NA
vg0818178441 sf0818175728 8 18178441 1.11E-06 NA
vg0900106167 sf0900105167 9 106167 NA 5.39E-06
vg0405873164 sf0405868605 4 5873164 NA 9.72E-06