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 mr1082 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
vg0718993421 sf0718992428 7 18993421 NA 5.76E-10
vg0719133785 sf0719132792 7 19133785 NA 6.71E-10
vg1202005433 sf1202004431 12 2005433 NA 5.73E-08
vg0706814672 sf0706813677 7 6814672 NA 2.16E-07
vg0719136249 sf0719135256 7 19136249 NA 4.66E-07
vg0315250141 sf0315248788 3 15250141 NA 4.76E-07
vg0610532521 sf0610531522 6 10532521 NA 7.44E-07
vg0719369036 sf0719368043 7 19369036 NA 8.12E-07
vg0720355169 sf0720354176 7 20355169 NA 1.19E-06
vg0428089846 sf0427904712 4 28089846 NA 2.33E-06
vg0719789133 sf0719788140 7 19789133 NA 2.39E-06
vg0720078741 sf0720077748 7 20078741 NA 2.50E-06
vg0315179985 sf0315178632 3 15179985 NA 3.05E-06
vg0608528871 sf0608527872 6 8528871 NA 4.11E-06
vg0431362633 sf0431177528 4 31362633 NA 4.44E-06