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 mr1404 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
vg0719039736 sf0719038743 7 19039736 2.09E-24 7.71E-20
vg0719063677 sf0719062684 7 19063677 2.60E-24 7.88E-20
vg0811938486 sf0811937491 8 11938486 1.39E-09 8.48E-06
vg0820065663 sf0820062950 8 20065663 1.65E-09 2.72E-07
vg1222822194 sf1222788633 12 22822194 5.85E-09 5.71E-06
vg0204849020 sf0204849017 2 4849020 1.26E-08 NA
vg0138727130 sf0138726087 1 38727130 5.72E-08 2.79E-07
vg1127413102 sf1126941489 11 27413102 7.03E-08 1.45E-06
vg0724265685 sf0724264691 7 24265685 4.68E-07 1.01E-06
vg0422772120 sf0422587003 4 22772120 1.04E-06 1.58E-06