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 mr1069 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
vg1222921847 sf1222888306 12 22921847 8.64E-10 2.47E-06
vg0135583115 sf0135582072 1 35583115 1.87E-08 NA
vg0405776502 sf0405771941 4 5776502 2.04E-08 NA
vg0728884022 sf0728883030 7 28884022 2.30E-08 9.18E-07
vg0112152317 sf0112151291 1 12152317 3.62E-08 NA
vg0300180852 sf0300179852 3 180852 6.82E-08 2.23E-07
vg0124176064 sf0124175020 1 24176064 1.57E-07 5.69E-08
vg0816013687 sf0816010973 8 16013687 2.43E-07 NA
vg0907048512 sf0907047512 9 7048512 4.38E-07 2.77E-06
vg1002920436 sf1002919413 10 2920436 1.77E-06 1.86E-06
vg0221017633 sf0221011765 2 21017633 8.75E-06 4.13E-06
vg1222876583 sf1222843023 12 22876583 9.08E-06 NA
vg1004612584 sf1004629122 10 4612584 NA 4.42E-06