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 mr1691 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
vg0721064561 sf0721063568 7 21064561 5.92E-09 1.78E-06
vg0722679457 sf0722678464 7 22679457 9.65E-09 NA
vg0912341273 sf0912340272 9 12341273 1.37E-08 NA
vg1009543409 sf1009472230 10 9543409 7.52E-08 NA
vg1017322255 sf1017251028 10 17322255 1.07E-06 NA
vg0711195681 sf0711194687 7 11195681 NA 2.20E-06
vg0511023890 sf0511023819 5 11023890 NA 4.26E-06