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 mr1612 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
vg0524346743 sf0524284164 5 24346743 9.17E-20 1.82E-13
vg0524382177 sf0524319598 5 24382177 1.46E-19 5.07E-14
vg0524409418 sf0524346839 5 24409418 2.85E-13 5.57E-10
vg0128647483 sf0128646438 1 28647483 4.89E-13 NA
vg0208009640 sf0208009639 2 8009640 1.42E-12 NA
vg0501421653 sf0501421637 5 1421653 2.76E-12 NA
vg0221243033 sf0221237165 2 21243033 1.88E-11 3.87E-06
vg0517780444 sf0517719930 5 17780444 5.22E-10 4.35E-06
vg0216629376 sf0216623506 2 16629376 2.77E-08 4.44E-07
vg1120967837 sf1120501710 11 20967837 1.19E-07 2.85E-06
vg0216620806 sf0216614936 2 16620806 NA 3.10E-07
vg0421497689 sf0421325740 4 21497689 NA 3.36E-07
vg0525524219 sf0525461640 5 25524219 NA 6.01E-07
vg1215581638 sf1215578935 12 15581638 NA 6.44E-07
vg1115774318 sf1115310627 11 15774318 NA 7.73E-07
vg0616757478 sf0616756480 6 16757478 NA 1.81E-06
vg0405830585 sf0405826024 4 5830585 NA 3.93E-06