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 mr1439 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
vg0320115825 sf0320114336 3 20115825 5.48E-09 3.09E-07
vg0320174856 sf0320173367 3 20174856 1.46E-08 1.93E-06
vg0121584750 sf0121583705 1 21584750 6.06E-08 NA
vg0318673691 sf0318672473 3 18673691 1.83E-07 4.02E-08
vg0141848695 sf0141847652 1 41848695 1.09E-06 NA
vg0406883539 sf0406878798 4 6883539 3.36E-06 4.55E-06
vg1218040492 sf1218011928 12 18040492 NA 6.48E-07
vg0616370853 sf0616369855 6 16370853 NA 1.56E-06
vg1205811494 sf1205810476 12 5811494 NA 2.56E-06
vg0307401131 sf0307400129 3 7401131 NA 4.96E-06