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 mr1304 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
vg0726837546 sf0726836552 7 26837546 9.47E-08 NA
vg0408995582 sf0408990858 4 8995582 9.53E-08 NA
vg0410451065 sf0410441764 4 10451065 1.31E-07 7.55E-06
vg1106375766 sf1106371518 11 6375766 5.43E-07 3.31E-07
vg0823213341 sf0823210628 8 23213341 1.64E-06 2.21E-06
vg0119598439 sf0119597394 1 19598439 5.94E-06 NA
vg0421558945 sf0421386995 4 21558945 NA 4.76E-06