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 mr1330 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
vg0138112582 sf0138111539 1 38112582 8.69E-22 NA
vg1021873088 sf1021801564 10 21873088 7.33E-20 NA
vg0135548077 sf0135547034 1 35548077 1.58E-19 NA
vg0141746853 sf0141745810 1 41746853 2.06E-19 NA
vg0132488834 sf0132487790 1 32488834 5.97E-19 NA
vg0141691238 sf0141690195 1 41691238 4.92E-17 NA
vg0724677672 sf0724676678 7 24677672 4.37E-15 NA
vg0504689285 sf0504689262 5 4689285 1.71E-14 NA
vg0603555760 sf0603554761 6 3555760 NA 2.65E-06
vg1208637169 sf1208634576 12 8637169 NA 7.67E-06
vg1126576144 sf1126104559 11 26576144 NA 7.71E-06