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 mr1408 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
vg0900499731 sf0900498731 9 499731 2.37E-11 3.20E-07
vg0217728046 sf0217722176 2 17728046 7.07E-10 2.45E-08
vg0719052097 sf0719051104 7 19052097 1.52E-09 3.87E-06
vg0704558652 sf0704557653 7 4558652 1.79E-09 1.99E-06
vg0216351821 sf0216345951 2 16351821 3.96E-09 7.81E-07
vg0617811733 sf0617810736 6 17811733 2.42E-08 2.80E-06
vg0620535795 sf0620534798 6 20535795 6.17E-08 5.78E-07
vg0407629615 sf0407624882 4 7629615 9.49E-08 5.99E-07
vg0407630134 sf0407625401 4 7630134 1.60E-07 4.27E-07
vg0900634520 sf0900633520 9 634520 4.99E-07 4.81E-06
vg0322556933 sf0322555422 3 22556933 1.34E-06 NA
vg0707768545 sf0707767550 7 7768545 2.74E-06 6.74E-06
vg0624163132 sf0624162135 6 24163132 NA 2.17E-06
vg1216729892 sf1216723846 12 16729892 NA 2.28E-06