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 mr1077 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
vg0222742146 sf0222736277 2 22742146 7.56E-46 1.51E-28
vg0222739831 sf0222733962 2 22739831 8.81E-45 1.76E-28
vg0223663746 sf0223657877 2 23663746 1.07E-16 5.49E-08
vg0223663745 sf0223657876 2 23663745 2.97E-16 2.74E-08
vg1112606104 sf1112142307 11 12606104 8.92E-15 NA
vg0600807366 sf0600806367 6 807366 8.07E-14 NA
vg0223079236 sf0223073367 2 23079236 1.94E-13 1.54E-06
vg0224640486 sf0224634617 2 24640486 3.31E-13 NA
vg0600805043 sf0600804044 6 805043 4.05E-12 NA
vg0224382271 sf0224376402 2 24382271 5.23E-12 2.50E-07
vg0223007097 sf0223001228 2 23007097 8.31E-12 1.11E-06
vg0226003155 sf0225997286 2 26003155 5.71E-10 4.08E-06
vg0222799001 sf0222793132 2 22799001 5.69E-08 5.86E-07
vg0222672664 sf0222666795 2 22672664 NA 4.97E-09
vg0610548373 sf0610547374 6 10548373 NA 3.24E-06