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 mr1779 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
vg1218054771 sf1218026207 12 18054771 6.30E-13 1.17E-07
vg0308360382 sf0308359320 3 8360382 1.99E-11 2.55E-06
vg0308428144 sf0308427082 3 8428144 2.39E-11 2.38E-06
vg0910413881 sf0910412880 9 10413881 1.18E-10 6.65E-06
vg0207238898 sf0207238898 2 7238898 1.55E-10 NA
vg0133079922 sf0133078878 1 33079922 2.01E-10 NA
vg1101519635 sf1101518636 11 1519635 1.58E-08 NA
vg0324008479 sf0324006653 3 24008479 8.75E-08 NA
vg0308476883 sf0308475821 3 8476883 NA 1.52E-07
vg0402100710 sf0402096304 4 2100710 NA 3.00E-06