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 mr1056 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
vg0433930554 sf0433745450 4 33930554 1.26E-10 2.81E-08
vg0526967577 sf0526904933 5 26967577 2.19E-10 NA
vg1015729829 sf1015658599 10 15729829 5.16E-10 NA
vg0630899696 sf0630898698 6 30899696 2.36E-09 NA
vg0120090794 sf0120089749 1 20090794 2.97E-09 NA
vg1118776907 sf1118310715 11 18776907 9.93E-09 2.24E-06
vg1208090350 sf1208087756 12 8090350 1.11E-08 4.84E-07
vg0522604659 sf0522542102 5 22604659 6.21E-08 1.61E-06
vg0224285961 sf0224280092 2 24285961 1.65E-07 2.37E-06
vg0527579554 sf0527516911 5 27579554 1.55E-06 NA
vg0804076961 sf0804075964 8 4076961 NA 1.83E-06