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 mr1322 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
vg0142781339 sf0142780295 1 42781339 6.68E-14 NA
vg0208901892 sf0208901890 2 8901892 1.46E-13 9.29E-06
vg0519281720 sf0519219204 5 19281720 9.85E-13 NA
vg1022038060 sf1021966535 10 22038060 1.66E-12 NA
vg0907434724 sf0907433724 9 7434724 2.02E-12 NA
vg0101289411 sf0101288411 1 1289411 3.44E-12 2.35E-06
vg0411353830 sf0411344533 4 11353830 1.05E-11 NA
vg0519817077 sf0519754561 5 19817077 2.04E-10 NA
vg0205031937 sf0205031934 2 5031937 1.45E-09 1.82E-06
vg0724425651 sf0724424657 7 24425651 4.73E-09 NA
vg0107647091 sf0107646091 1 7647091 NA 2.71E-07
vg0519159149 sf0519096633 5 19159149 NA 4.98E-06