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 mr1412 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
vg0819603039 sf0819600326 8 19603039 2.97E-09 2.97E-09
vg0122971925 sf0122970881 1 22971925 9.92E-08 9.93E-08
vg0127428591 sf0127427547 1 27428591 9.54E-07 9.54E-07
vg0704732672 sf0704731673 7 4732672 1.32E-06 1.32E-06
vg0805826839 sf0805825842 8 5826839 1.46E-06 1.46E-06
vg0421030366 sf0420858419 4 21030366 1.73E-06 1.73E-06
vg0409914634 sf0409905332 4 9914634 2.08E-06 2.08E-06
vg0717084739 sf0717083746 7 17084739 4.31E-06 4.31E-06
vg0407320870 sf0407316140 4 7320870 4.31E-06 4.32E-06
vg0819985140 sf0819982427 8 19985140 4.63E-06 4.63E-06