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 mr1425 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
vg1017105232 sf1017034004 10 17105232 4.77E-09 NA
vg1006698817 sf1006714440 10 6698817 1.54E-08 NA
vg1002807953 sf1002806930 10 2807953 2.74E-08 NA
vg0815658197 sf0815655483 8 15658197 3.01E-08 NA
vg0821534137 sf0821531424 8 21534137 4.13E-08 NA
vg0909993670 sf0909992669 9 9993670 4.26E-08 NA
vg0410648777 sf0410639477 4 10648777 5.06E-08 3.65E-06
vg0802255218 sf0802254221 8 2255218 2.51E-07 2.25E-06
vg0813446827 sf0813444380 8 13446827 3.85E-06 3.11E-06
vg0129713873 sf0129712828 1 29713873 NA 5.05E-06