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 mr1805 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
vg1210561791 sf1210559204 12 10561791 1.66E-13 NA
vg0601445283 sf0601444284 6 1445283 2.09E-13 NA
vg1214145353 sf1214142693 12 14145353 2.77E-12 NA
vg0200214149 sf0200214149 2 214149 1.07E-10 NA
vg1205430972 sf1205429958 12 5430972 1.09E-10 NA
vg1210856629 sf1210853995 12 10856629 1.16E-10 NA
vg0528622478 sf0528559833 5 28622478 4.09E-10 2.93E-06
vg0320153257 sf0320151768 3 20153257 4.62E-08 1.87E-06
vg0200471574 sf0200471574 2 471574 5.47E-07 2.95E-06
vg0200348780 sf0200348780 2 348780 NA 2.84E-06
vg0906931088 sf0906930088 9 6931088 NA 3.69E-06
vg0907268757 sf0907267757 9 7268757 NA 7.19E-06