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 mr1781 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
vg0402217448 sf0402213043 4 2217448 1.16E-09 3.22E-08
vg1219830048 sf1219801518 12 19830048 1.12E-08 8.88E-06
vg0223858890 sf0223853021 2 23858890 1.76E-08 5.21E-06
vg1221621581 sf1221588128 12 21621581 2.54E-08 NA
vg0402179892 sf0402175487 4 2179892 4.00E-07 4.81E-06
vg0407068622 sf0407063893 4 7068622 4.53E-07 4.94E-06
vg1219713642 sf1219685112 12 19713642 5.31E-07 NA
vg0429731545 sf0429546415 4 29731545 7.54E-07 NA
vg0816277211 sf0816274497 8 16277211 1.12E-06 4.71E-06
vg1007047646 sf1007063269 10 7047646 3.88E-06 1.56E-06