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 mr1243 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
vg0216744504 sf0216738634 2 16744504 9.59E-14 NA
vg0216568221 sf0216562351 2 16568221 1.99E-13 NA
vg0216649473 sf0216643603 2 16649473 4.32E-13 4.71E-06
vg1108725515 sf1108720125 11 8725515 6.05E-12 NA
vg0216909425 sf0216903555 2 16909425 9.39E-12 NA
vg0515519848 sf0515462389 5 15519848 2.58E-10 NA
vg1121837830 sf1121371707 11 21837830 1.36E-09 NA
vg0621384427 sf0621383430 6 21384427 1.38E-09 NA
vg1117082364 sf1116616216 11 17082364 4.89E-07 NA
vg1222100421 sf1222066968 12 22100421 6.39E-07 NA