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 mr1830 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
vg0218455087 sf0218449218 2 18455087 1.46E-20 NA
vg0411407679 sf0411398382 4 11407679 1.48E-19 NA
vg0310702180 sf0310701096 3 10702180 1.48E-19 NA
vg0310762438 sf0310761354 3 10762438 2.26E-19 7.21E-06
vg0723097242 sf0723096249 7 23097242 5.90E-19 NA
vg0204395461 sf0204395458 2 4395461 1.04E-18 NA
vg0307904956 sf0307903894 3 7904956 5.76E-17 3.79E-06
vg0216483675 sf0216477805 2 16483675 3.18E-16 NA
vg0409475911 sf0409466609 4 9475911 NA 5.63E-07
vg0207214257 sf0207214257 2 7214257 NA 1.08E-06