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 mr1225 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
vg0719006030 sf0719005037 7 19006030 4.55E-49 2.97E-14
vg0719124635 sf0719123642 7 19124635 3.41E-40 1.77E-16
vg1107671210 sf1107666955 11 7671210 5.69E-40 2.51E-07
vg1201345845 sf1201344845 12 1345845 2.81E-37 NA
vg0305023072 sf0305022074 3 5023072 3.36E-36 NA
vg0435366429 sf0435181311 4 35366429 6.06E-36 NA
vg0617272557 sf0617271560 6 17272557 2.85E-32 NA
vg0718999754 sf0718998761 7 18999754 7.15E-31 3.85E-06
vg0222752747 sf0222746878 2 22752747 NA 4.78E-14
vg0222752123 sf0222746254 2 22752123 NA 8.03E-14
vg0719091461 sf0719090468 7 19091461 NA 5.03E-12
vg0719345307 sf0719344314 7 19345307 NA 2.57E-10
vg0222816080 sf0222810211 2 22816080 NA 2.21E-09
vg0719346699 sf0719345706 7 19346699 NA 4.43E-08
vg0719079053 sf0719078060 7 19079053 NA 4.79E-08
vg0719413496 sf0719412503 7 19413496 NA 6.35E-07
vg1115764925 sf1115301234 11 15764925 NA 6.56E-07
vg0719466615 sf0719465622 7 19466615 NA 9.35E-07
vg0718890254 sf0718889261 7 18890254 NA 2.31E-06
vg0718922665 sf0718921672 7 18922665 NA 2.63E-06