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 mr1380 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
vg0123687464 sf0123686420 1 23687464 1.28E-13 NA
vg1126520429 sf1126048844 11 26520429 1.27E-12 9.38E-06
vg0300484981 sf0300483979 3 484981 1.47E-12 NA
vg0300483843 sf0300482841 3 483843 2.47E-12 3.29E-06
vg0123578067 sf0123577023 1 23578067 7.45E-12 4.47E-06
vg1126542743 sf1126071158 11 26542743 4.14E-11 1.31E-09
vg0123307230 sf0123306186 1 23307230 4.17E-11 NA
vg1127031755 sf1126560142 11 27031755 8.06E-11 1.03E-06
vg0808371714 sf0808370718 8 8371714 2.24E-07 NA
vg0122413949 sf0122412904 1 22413949 7.83E-07 NA
vg0625306076 sf0625305079 6 25306076 1.06E-06 NA