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 mr1764 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 1.01E-09 1.02E-09
vg0816860448 sf0816857734 8 16860448 3.37E-07 3.37E-07
vg0820873126 sf0820870413 8 20873126 5.81E-07 5.81E-07
vg0127428591 sf0127427547 1 27428591 6.67E-07 6.67E-07
vg0717084739 sf0717083746 7 17084739 1.16E-06 1.16E-06
vg0409914634 sf0409905332 4 9914634 1.16E-06 1.16E-06
vg0410534481 sf0410525180 4 10534481 1.99E-06 1.99E-06
vg1216966466 sf1216960420 12 16966466 2.03E-06 2.03E-06
vg0113601070 sf0113600044 1 13601070 2.91E-06 2.91E-06
vg1104063322 sf1104059224 11 4063322 3.19E-06 3.19E-06
vg0122971925 sf0122970881 1 22971925 3.48E-06 3.48E-06