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 mr1598 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
vg0918924718 sf0918923718 9 18924718 2.71E-29 2.74E-15
vg0918496669 sf0918495668 9 18496669 1.54E-23 3.28E-12
vg0919489582 sf0919489172 9 19489582 2.05E-18 2.13E-07
vg0235055826 sf0235049957 2 35055826 1.00E-16 NA
vg0919909414 sf0919908933 9 19909414 1.18E-15 NA
vg1109851703 sf1109846280 11 9851703 7.71E-15 NA
vg0919233052 sf0919232642 9 19233052 2.17E-14 1.77E-07
vg0918589964 sf0918588963 9 18589964 2.02E-11 4.86E-10
vg0912275276 sf0912274275 9 12275276 9.69E-11 9.96E-07
vg0918597790 sf0918596789 9 18597790 9.62E-10 3.51E-09
vg0123033739 sf0123032695 1 23033739 NA 6.60E-07
vg0919142743 sf0919142332 9 19142743 NA 1.89E-06
vg0917357322 sf0917356321 9 17357322 NA 2.16E-06
vg0212200339 sf0212200335 2 12200339 NA 4.02E-06