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 mr1993 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
vg0216064452 sf0216058582 2 16064452 3.96E-11 NA
vg0617843351 sf0617842354 6 17843351 4.53E-11 2.34E-06
vg1100952658 sf1100951659 11 952658 1.17E-10 NA
vg0820148135 sf0820145422 8 20148135 1.21E-10 NA
vg1017841254 sf1017770027 10 17841254 3.18E-10 NA
vg0614456600 sf0614455601 6 14456600 NA 2.90E-06
vg1216930812 sf1216924766 12 16930812 NA 3.39E-06