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 mr1511 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
vg0821970212 sf0821967499 8 21970212 2.16E-09 6.57E-07
vg0128902126 sf0128901081 1 28902126 4.17E-08 4.66E-07
vg0131535738 sf0131534694 1 31535738 2.49E-07 2.18E-06
vg0820796944 sf0820794231 8 20796944 7.85E-07 1.32E-06
vg1010547694 sf1010476515 10 10547694 9.50E-07 2.82E-06
vg0119898952 sf0119897907 1 19898952 3.34E-06 NA
vg1224677166 sf1224643620 12 24677166 4.76E-06 NA