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 mr1481 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
vg1122514350 sf1122048221 11 22514350 1.26E-08 1.26E-08
vg0612029845 sf0612028846 6 12029845 2.59E-07 2.60E-07
vg1121947207 sf1121481078 11 21947207 4.75E-07 4.76E-07
vg0212840665 sf0212840661 2 12840665 1.27E-06 1.28E-06
vg0529093514 sf0529030869 5 29093514 1.71E-06 1.71E-06
vg0507563644 sf0507563585 5 7563644 2.52E-06 2.52E-06
vg0422542724 sf0422357611 4 22542724 4.12E-06 4.13E-06